Genetic Variant KRTAP5-10:p.Gly102Trp (chr11-71565891-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001012710.2(KRTAP5-10):c.304G>T(p.Gly102Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00047 ( 0 hom., cov: 17)

Exomes 𝑓: 0.00095 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

KRTAP5-10
NM_001012710.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.528

Variant links:

Genes affected

KRTAP5-10 (HGNC:23605): (keratin associated protein 5-10) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP5-10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.069520354).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTAP5-10	NM_001012710.2 link	c.304G>T	p.Gly102Trp	missense_variant	Exon 1 of 1	ENST00000398531.3	NP_001012728.1	Q6L8G5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTAP5-10	ENST00000398531.3 link	c.304G>T	p.Gly102Trp	missense_variant	Exon 1 of 1	6	NM_001012710.2	ENSP00000381542.1		Q6L8G5

Frequencies

GnomAD3 genomes

AF:

0.000468

AC:

AN:

119762

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000226

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000869

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000661

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000780

Gnomad OTH

AF:

0.000639

GnomAD3 exomes

AF:

0.000570

AC:

138

AN:

242186

Hom.:

AF XY:

0.000555

AC XY:

AN XY:

131418

show subpopulations

Gnomad AFR exome

AF:

0.000201

Gnomad AMR exome

AF:

0.000324

Gnomad ASJ exome

AF:

0.000209

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.000334

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00100

Gnomad OTH exome

AF:

0.000170

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000954

AC:

1169

AN:

1225364

Hom.:

Cov.:

AF XY:

0.000955

AC XY:

580

AN XY:

607070

show subpopulations

Gnomad4 AFR exome

AF:

0.0000378

Gnomad4 AMR exome

AF:

0.000172

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000507

Gnomad4 FIN exome

AF:

0.0000509

Gnomad4 NFE exome

AF:

0.00114

Gnomad4 OTH exome

AF:

0.000846

GnomAD4 genome

AF:

0.000467

AC:

AN:

119846

Hom.:

Cov.:

AF XY:

0.000436

AC XY:

AN XY:

57386

show subpopulations

Gnomad4 AFR

AF:

0.000225

Gnomad4 AMR

AF:

0.0000868

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000662

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000780

Gnomad4 OTH

AF:

0.000635

Alfa

AF:

0.000767

Hom.:

ESP6500AA

AF:

0.000235

AC:

ESP6500EA

AF:

0.000824

AC:

ExAC

AF:

0.000374

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Aug 07, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.304G>T (p.G102W) alteration is located in exon 1 (coding exon 1) of the KRTAP5-10 gene. This alteration results from a G to T substitution at nucleotide position 304, causing the glycine (G) at amino acid position 102 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.42

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.62

DEOGEN2

Benign

0.078

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.37

M_CAP

Benign

0.0031

MetaRNN

Benign

0.070

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.4

PROVEAN

Benign

-1.6

REVEL

Benign

0.13

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.011

Polyphen

1.0

Vest4

0.27

MVP

0.030

MPC

0.0083

ClinPred

0.090

GERP RS

1.9

Varity_R

0.040

gMVP

0.027

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over