Table of Contents : Managing variants :
Entering variants | Variants annotations | Importing variants | Exporting & reporting variants

Variant Annotations

Alamut® Visual provides for each variant a list of annotations for use by external applications. See Exporting and Reporting Variants.

Annotation Catalog

Annotation Name Example Comment

Gene symbol gene MLH1 Official HGNC symbol

Gene id (HGNC) geneId 7127

Chromosome chrom 3

Transcript transcript NM_000249.3 Transcript used for annotations

Strand strand 1 1/-1

Protein protein NP_000240.1

Uniprot accession Uniprot P40692

Variant Type varType substitution Possible values: substitution, deletion, insertion, duplication, delins

Variant coding effect codingEffect missense Possible values: synonymous, missense, stop gain, in-frame, frameshift, start loss, stop loss

Variant location varLocation exon Possible values: upstream, 5'UTR, exon, intron, 3'UTR, downstream

Genome assembly assembly GRCh37 For RefSeqGene and LRG sequences: sequence id, e.g.: NG_016740.1, LRG_1.

gDNA start gDNAstart 37090074

gDNA end gDNAend 37090074

Genomic-level nomenclature gNomen g.37090074A>G

cDNA start cDNAstart 1963

cDNA end cDNAend 1963

CDNA-level nomenclature cNomen c.1963A>G

Protein-level nomenclature pNomen p.Ile655Val

Alternate protein-level nomenclature alt_pNomen p.Ile655Val Like pNomen except for syn. variants: p.Leu123Leu

Exon exon 17 Nearest exon number if intronic variant

Intron intron

OMIM® id omimId 120436

User-specified pathogenicity class pathogenicityClass Class 3-Unknown pathogenicity

Distance to nearest splice site distNearestSS -27

Nearest splice site type nearestSSType 5' Possible values: 5', 3'

WT seq. SpliceSiteFinder score wtSSFScore 87.0628 Predictions at nearest splice site

WT seq. MaxEntScan score wtMaxEntScore 7.69979 idem

WT seq. NNSPLICE score wtNNSScore 0.910784 idem

WT seq. GeneSplicer score wtGSScore 1.99619 idem

Variant seq. SpliceSiteFinder score varSSFScore 87.0628 idem

Variant seq. MaxEntScan score varMaxEntScore 7.69979 idem

Variant seq. NNSPLICE score varNNSScore 0.910784 idem

Variant seq. GeneSplicer score varGSScore 2.29216 idem

Average change at nearest splice site nearestSSChange 0 Average change predicted by MaxEntScan, NNSPLICE, and SSF

Predicted splice site effect in the immediate variant vicinity localSpliceEffect Cryptic Acceptor Strongly Activated Possible values: Cryptic Donor Strongly Activated, Cryptic Donor Weakly Activated, Cryptic Acceptor Strongly Activated, Cryptic Acceptor Weakly Activated, New Donor Site, New Acceptor Site

Protein domain 1 proteinDomain1

Protein domain 2 proteinDomain2

Protein domain 3 proteinDomain3

Protein domain 4 proteinDomain4

dbSNP variation rsId rs55907433

dbSNP validated variation? rsValidated yes Possible values: yes, no

dbSNP suspect variation? rsSuspect no Possible values: yes/no � Variant flagged as suspect by dbSNP

dbSNP validation labels rsValidations Cluster/Frequency/1000G

dbSNP number of validation categories rsValidationNumber

dbSNP variation ancestral allele rsAncestralAllele A,A,A,A

dbSNP variation average heterozygosity rsHeterozygosity 0.010

dbSNP variation clinical significance rsClinicalSignificance untested

dbSNP variation global Minor Allele Frequency rsMAF 0.003

dbSNP variation global minor allele rsMAFAllele G

dbSNP variation sample size rsMAFCount 2184

gnomAD call quality gnomadQuality 0.000

gnomAD filter status gnomadFilter PASS

gnomAD alternate allele count gnomadAlleleCount 131

gnomAD alternate allele frequency in All population gnomadAllFreq 0.001

gnomAD alternate allele frequency in African population gnomadAFRFreq 0.009
gnomAD alternate allele frequency in Latino population gnomadAMRFreq 0.001

gnomAD alternate allele frequency in Ashkenazi Jewish population gnomadASJFreq 0.001

gnomAD alternate allele frequency in East Asian population gnomadEASFreq 0.000

gnomAD alternate allele frequency in South Asian population gnomadSASFreq 0.000

gnomAD alternate allele frequency in European (Non-Finnish) population gnomadNFEFreq 0.001

gnomAD alternate allele frequency in Finnish (European) population gnomadFINFreq 0.000

gnomAD alternate allele frequency in Other population gnomadOTHFreq 0.000

gnomAD estimated read depth gnomadDP 45

ESP reference allele counts in European American population espRefEACount

ESP reference allele count in African American population espRefAACount

ESP reference allele count in all populations espRefAllCount

ESP alternate allele count in European American population espAltEACount

ESP alternate allele count in African American population espAltAACount

ESP alternate allele count in all populations espAltAllCount

Minor allele frequency in European American population espEAMAF

Minor allele frequency in African American population espAAMAF

Minor allele frequency in all populations espAllMAF

Alternate allele frequency in European American population espEAAAF

Alternate allele frequency in African American population espAAAAF

Alternate allele frequency in all populations espAllAAF

Average sample read depth espAvgReadDepth

ClinVar Variant ids
(each record is delimited by vertical bars "|") clinVarIds

ClinVar Variant origins
(each record is delimited by vertical bars "|") clinVarOrigins

ClinVar Variant methods
(each record is delimited by vertical bars "|") clinVarMethods

ClinVar Variant clinical significance
(each record is delimited by vertical bars "|") clinVarClinSignifs

ClinVar Variant review status
(each record is delimited by vertical bars "|") clinVarReviewStatus

ClinVar Variant condition names
(each record is delimited by vertical bars "|") clinVarPhenotypes

Cosmic Variant ids
(each record is delimited by vertical bars "|") cosmicIds

Cosmic Variant tissues
(each record is delimited by vertical bars "|") cosmicTissues

Substitutions

Type substType transition Possible values: transition, transversion

WT nucleotide wtNuc A

Variant nucleotide varNuc G

Nucleotide change nucChange A>G

PhastCons score phastCons 0.236

phyloP score phyloP 0.367

All coding substitutions

WT AA (1 letter) wtAA_1 I

WT AA (3 letters) wtAA_3 Ile

WT codon wtCodon ATC

WT codon frequency wtCodonFreq 0.481

Variant AA (1 letter) varAA_1 V

Variant AA (3 letters) varAA_3 Val

Variant codon varCodon GTC

Variant codon frequency varCodonFreq 0.240

AA Position posAA 655

Missense only

Number of orthologues in alignment nOrthos 11

Number of conserved residues in alignment conservedOrthos 6

Most distant species in which AA is conserved conservedDistSpecies Horse

BLOSUM45 BLOSUM45 -3

BLOSUM62 BLOSUM62 -3

BLOSUM80 BLOSUM80 4

WT AA composition wtAAcomposition 0

Variant AA composition varAAcomposition 0

WT AA polarity wtAApolarity 5.2

Variant AA polarity varAApolarity 5.9

WT AA volume wtAAvolume 111

Variant AA volume varAAvolume 84

Grantham distance granthamDist 29

AlignGVGD class AGVGDclass C0

AlignGVGD: variation (GV) AGVGDgv 50.29

AlignGVGD: deviation (GD) AGVGDgd 0

SIFT prediction SIFTprediction Tolerated

SIFT weight SIFTweight 0.64

SIFT median SIFTmedian 3.33

PolyPhen-2 prediction PPH2prediction Qualitative ternary classification at 10%/20% (20%/40% for HumVar) FPR thresholds (benign, possibly damaging, probably damaging)

PolyPhen-2 class PPH2class Probabilistic binary classifier outcome (damaging or neutral)

PolyPhen-2 score PPH2score Classifier probability of the variation being damaging

MAPP prediction MAPPprediction good

MAPP p-value MAPPpValue 1.23E-1

MAPP p-value median MAPPpValueMedian 0.02452

MutationTaster prediction TASTERprediction polymorphism

MutationTaster p-value TASTERpValue 0.999

Occurrences Available only for internal variants

Patient ID patient.id

Family ID patient.family

Comment patient.comment

Phenotype patient.phenotype

RNA Analysis patient.rnaAnalysis

Created patient.createdDate

Updated patient.updatedDate

User information Available only for internal variants

Institution user.institution

Initials user.initials

Annotation	Name	Example	Comment
Gene symbol	gene	MLH1	Official HGNC symbol
Gene id (HGNC)	geneId	7127
Chromosome	chrom	3
Transcript	transcript	NM_000249.3	Transcript used for annotations
Strand	strand	1	1/-1
Protein	protein	NP_000240.1
Uniprot accession	Uniprot	P40692
Variant Type	varType	substitution	Possible values: substitution, deletion, insertion, duplication, delins
Variant coding effect	codingEffect	missense	Possible values: synonymous, missense, stop gain, in-frame, frameshift, start loss, stop loss
Variant location	varLocation	exon	Possible values: upstream, 5'UTR, exon, intron, 3'UTR, downstream
Genome assembly	assembly	GRCh37	For RefSeqGene and LRG sequences: sequence id, e.g.: NG_016740.1, LRG_1.
gDNA start	gDNAstart	37090074
gDNA end	gDNAend	37090074
Genomic-level nomenclature	gNomen	g.37090074A>G
cDNA start	cDNAstart	1963
cDNA end	cDNAend	1963
CDNA-level nomenclature	cNomen	c.1963A>G
Protein-level nomenclature	pNomen	p.Ile655Val
Alternate protein-level nomenclature	alt_pNomen	p.Ile655Val	Like pNomen except for syn. variants: p.Leu123Leu
Exon	exon	17	Nearest exon number if intronic variant
Intron	intron
OMIM® id	omimId	120436
User-specified pathogenicity class	pathogenicityClass	Class 3-Unknown pathogenicity

Distance to nearest splice site	distNearestSS	-27
Nearest splice site type	nearestSSType	5'	Possible values: 5', 3'
WT seq. SpliceSiteFinder score	wtSSFScore	87.0628	Predictions at nearest splice site
WT seq. MaxEntScan score	wtMaxEntScore	7.69979	idem
WT seq. NNSPLICE score	wtNNSScore	0.910784	idem
WT seq. GeneSplicer score	wtGSScore	1.99619	idem
Variant seq. SpliceSiteFinder score	varSSFScore	87.0628	idem
Variant seq. MaxEntScan score	varMaxEntScore	7.69979	idem
Variant seq. NNSPLICE score	varNNSScore	0.910784	idem
Variant seq. GeneSplicer score	varGSScore	2.29216	idem
Average change at nearest splice site	nearestSSChange	0	Average change predicted by MaxEntScan, NNSPLICE, and SSF
Predicted splice site effect in the immediate variant vicinity	localSpliceEffect	Cryptic Acceptor Strongly Activated	Possible values: Cryptic Donor Strongly Activated, Cryptic Donor Weakly Activated, Cryptic Acceptor Strongly Activated, Cryptic Acceptor Weakly Activated, New Donor Site, New Acceptor Site

Protein domain 1	proteinDomain1
Protein domain 2	proteinDomain2
Protein domain 3	proteinDomain3
Protein domain 4	proteinDomain4

dbSNP variation	rsId	rs55907433
dbSNP validated variation?	rsValidated	yes	Possible values: yes, no
dbSNP suspect variation?	rsSuspect	no	Possible values: yes/no � Variant flagged as suspect by dbSNP
dbSNP validation labels	rsValidations	Cluster/Frequency/1000G
dbSNP number of validation categories	rsValidationNumber
dbSNP variation ancestral allele	rsAncestralAllele	A,A,A,A
dbSNP variation average heterozygosity	rsHeterozygosity	0.010
dbSNP variation clinical significance	rsClinicalSignificance	untested
dbSNP variation global Minor Allele Frequency	rsMAF	0.003
dbSNP variation global minor allele	rsMAFAllele	G
dbSNP variation sample size	rsMAFCount	2184

gnomAD call quality	gnomadQuality	0.000
gnomAD filter status	gnomadFilter	PASS
gnomAD alternate allele count	gnomadAlleleCount	131
gnomAD alternate allele frequency in All population	gnomadAllFreq	0.001
gnomAD alternate allele frequency in African population	gnomadAFRFreq	0.009
gnomAD alternate allele frequency in Latino population	gnomadAMRFreq	0.001
gnomAD alternate allele frequency in Ashkenazi Jewish population	gnomadASJFreq	0.001
gnomAD alternate allele frequency in East Asian population	gnomadEASFreq	0.000
gnomAD alternate allele frequency in South Asian population	gnomadSASFreq	0.000
gnomAD alternate allele frequency in European (Non-Finnish) population	gnomadNFEFreq	0.001
gnomAD alternate allele frequency in Finnish (European) population	gnomadFINFreq	0.000
gnomAD alternate allele frequency in Other population	gnomadOTHFreq	0.000
gnomAD estimated read depth	gnomadDP	45

ESP reference allele counts in European American population	espRefEACount
ESP reference allele count in African American population	espRefAACount
ESP reference allele count in all populations	espRefAllCount
ESP alternate allele count in European American population	espAltEACount
ESP alternate allele count in African American population	espAltAACount
ESP alternate allele count in all populations	espAltAllCount
Minor allele frequency in European American population	espEAMAF
Minor allele frequency in African American population	espAAMAF
Minor allele frequency in all populations	espAllMAF
Alternate allele frequency in European American population	espEAAAF
Alternate allele frequency in African American population	espAAAAF
Alternate allele frequency in all populations	espAllAAF
Average sample read depth	espAvgReadDepth

ClinVar Variant ids (each record is delimited by vertical bars "\|")	clinVarIds
ClinVar Variant origins (each record is delimited by vertical bars "\|")	clinVarOrigins
ClinVar Variant methods (each record is delimited by vertical bars "\|")	clinVarMethods
ClinVar Variant clinical significance (each record is delimited by vertical bars "\|")	clinVarClinSignifs
ClinVar Variant review status (each record is delimited by vertical bars "\|")	clinVarReviewStatus
ClinVar Variant condition names (each record is delimited by vertical bars "\|")	clinVarPhenotypes

Cosmic Variant ids (each record is delimited by vertical bars "\|")	cosmicIds
Cosmic Variant tissues (each record is delimited by vertical bars "\|")	cosmicTissues

Substitutions
Type	substType	transition	Possible values: transition, transversion
WT nucleotide	wtNuc	A
Variant nucleotide	varNuc	G
Nucleotide change	nucChange	A>G
PhastCons score	phastCons	0.236
phyloP score	phyloP	0.367

All coding substitutions
WT AA (1 letter)	wtAA_1	I
WT AA (3 letters)	wtAA_3	Ile
WT codon	wtCodon	ATC
WT codon frequency	wtCodonFreq	0.481
Variant AA (1 letter)	varAA_1	V
Variant AA (3 letters)	varAA_3	Val
Variant codon	varCodon	GTC
Variant codon frequency	varCodonFreq	0.240
AA Position	posAA	655

Missense only
Number of orthologues in alignment	nOrthos	11
Number of conserved residues in alignment	conservedOrthos	6
Most distant species in which AA is conserved	conservedDistSpecies	Horse

BLOSUM45	BLOSUM45	-3
BLOSUM62	BLOSUM62	-3
BLOSUM80	BLOSUM80	4
WT AA composition	wtAAcomposition	0
Variant AA composition	varAAcomposition	0
WT AA polarity	wtAApolarity	5.2
Variant AA polarity	varAApolarity	5.9
WT AA volume	wtAAvolume	111
Variant AA volume	varAAvolume	84
Grantham distance	granthamDist	29

AlignGVGD class	AGVGDclass	C0
AlignGVGD: variation (GV)	AGVGDgv	50.29
AlignGVGD: deviation (GD)	AGVGDgd	0
SIFT prediction	SIFTprediction	Tolerated
SIFT weight	SIFTweight	0.64
SIFT median	SIFTmedian	3.33
PolyPhen-2 prediction	PPH2prediction		Qualitative ternary classification at 10%/20% (20%/40% for HumVar) FPR thresholds (benign, possibly damaging, probably damaging)
PolyPhen-2 class	PPH2class		Probabilistic binary classifier outcome (damaging or neutral)
PolyPhen-2 score	PPH2score		Classifier probability of the variation being damaging
MAPP prediction	MAPPprediction	good
MAPP p-value	MAPPpValue	1.23E-1
MAPP p-value median	MAPPpValueMedian	0.02452
MutationTaster prediction	TASTERprediction	polymorphism
MutationTaster p-value	TASTERpValue	0.999

Occurrences			Available only for internal variants
Patient ID	patient.id
Family ID	patient.family
Comment	patient.comment
Phenotype	patient.phenotype
RNA Analysis	patient.rnaAnalysis
Created	patient.createdDate
Updated	patient.updatedDate

User information			Available only for internal variants
Institution	user.institution
Initials	user.initials