Genetic Variant KRTAP2-2:p.Gly7Val (chr17-41055192-C-A) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_033032.3(KRTAP2-2):c.20G>T(p.Gly7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,419,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000068 ( 0 hom., cov: 28)

Exomes 𝑓: 0.000027 ( 1 hom. )

Consequence

KRTAP2-2
NM_033032.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.86

Publications

0 publications found

Variant links:

Genes affected

KRTAP2-2 (HGNC:18905): (keratin associated protein 2-2) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP2-2 links:

ENSG00000306126 (HGNC:):

ENSG00000306126 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.34656507).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033032.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP2-2	NM_033032.3	MANE Select	c.20G>T	p.Gly7Val	missense	Exon 1 of 1	NP_149021.2	Q9BYT5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KRTAP2-2	ENST00000398477.1	TSL:6 MANE Select	c.20G>T	p.Gly7Val	missense	Exon 1 of 1	ENSP00000381494.1	Q9BYT5
ENSG00000306126	ENST00000815517.1		n.220-5107C>A		intron	N/A
ENSG00000306126	ENST00000815518.1		n.160-5107C>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

146198

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000153

AC:

AN:

65552

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.000175

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000275

AC:

AN:

1273322

Hom.:

Cov.:

AF XY:

0.0000339

AC XY:

AN XY:

619554

show subpopulations

African (AFR)

AF:

0.000468

AC:

AN:

27756

American (AMR)

AF:

0.00

AC:

AN:

21198

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19006

East Asian (EAS)

AF:

0.00

AC:

AN:

34946

South Asian (SAS)

AF:

0.00

AC:

AN:

63352

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31056

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3594

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1019164

Other (OTH)

AF:

0.000413

AC:

AN:

53250

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.410

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000683

AC:

AN:

146312

Hom.:

Cov.:

AF XY:

0.0000141

AC XY:

AN XY:

71120

show subpopulations

African (AFR)

AF:

0.0000254

AC:

AN:

39314

American (AMR)

AF:

0.00

AC:

AN:

14518

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3414

East Asian (EAS)

AF:

0.00

AC:

AN:

4996

South Asian (SAS)

AF:

0.00

AC:

AN:

4340

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10050

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

66494

Other (OTH)

AF:

0.00

AC:

AN:

1998

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Benign

-0.27

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.031

Eigen

Uncertain

0.54

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.67

M_CAP

Benign

0.014

MetaRNN

Benign

0.35

MetaSVM

Benign

-0.98

MutationAssessor

Pathogenic

3.2

PhyloP100

1.9

PrimateAI

Uncertain

0.64

PROVEAN

Pathogenic

-5.2

REVEL

Benign

0.28

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.019

Vest4

0.37

MutPred

0.59

Loss of glycosylation at S4 (P = 0.0778)

MVP

0.55

ClinPred

0.90

GERP RS

5.5

PromoterAI

0.0088

Neutral

(source)

Varity_R

0.71

gMVP

0.15

Mutation Taster

=88/12

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over