Variant chr17-41097583-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_031960.3(KRTAP4-8):c.502G>A(p.Ala168Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 1,506,894 control chromosomes in the GnomAD database, including 303,204 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 34562 hom., cov: 28)

Exomes 𝑓: 0.62 ( 268642 hom. )

Consequence

KRTAP4-8
NM_031960.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0110

Variant links:

Genes affected

KRTAP4-8 (HGNC:17230): (keratin associated protein 4-8) Involved in aging and hair cycle. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP4-8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.5975036E-7).

BP6

Variant 17-41097583-C-T is Benign according to our data. Variant chr17-41097583-C-T is described in ClinVar as [Benign]. Clinvar id is 403023.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRTAP4-8	NM_031960.3 linkuse as main transcript	c.502G>A	p.Ala168Thr	missense_variant	1/1	ENST00000333822.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRTAP4-8	ENST00000333822.5 linkuse as main transcript	c.502G>A	p.Ala168Thr	missense_variant	1/1		NM_031960.3	P1

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

99113

AN:

146298

Hom.:

34519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.861

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.647

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.665

GnomAD3 exomes

AF:

0.565

AC:

84691

AN:

150016

Hom.:

27308

AF XY:

0.553

AC XY:

43590

AN XY:

78826

show subpopulations

Gnomad AFR exome

AF:

0.848

Gnomad AMR exome

AF:

0.543

Gnomad ASJ exome

AF:

0.630

Gnomad EAS exome

AF:

0.363

Gnomad SAS exome

AF:

0.465

Gnomad FIN exome

AF:

0.651

Gnomad NFE exome

AF:

0.580

Gnomad OTH exome

AF:

0.582

GnomAD4 exome

AF:

0.618

AC:

841204

AN:

1360484

Hom.:

268642

Cov.:

AF XY:

0.615

AC XY:

411784

AN XY:

669822

show subpopulations

Gnomad4 AFR exome

AF:

0.869

Gnomad4 AMR exome

AF:

0.567

Gnomad4 ASJ exome

AF:

0.646

Gnomad4 EAS exome

AF:

0.421

Gnomad4 SAS exome

AF:

0.514

Gnomad4 FIN exome

AF:

0.660

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.678

AC:

99203

AN:

146410

Hom.:

34562

Cov.:

AF XY:

0.673

AC XY:

48122

AN XY:

71516

show subpopulations

Gnomad4 AFR

AF:

0.860

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.647

Gnomad4 EAS

AF:

0.420

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.658

Gnomad4 NFE

AF:

0.627

Gnomad4 OTH

AF:

0.667

Alfa

AF:

0.634

Hom.:

5162

Bravo

AF:

0.697

ExAC

AF:

0.401

AC:

40734

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.057

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.81

DEOGEN2

Benign

0.00051

T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-0.95

FATHMM_MKL

Benign

0.035

LIST_S2

Benign

0.0071

T;T

MetaRNN

Benign

6.6e-7

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-2.0

N;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.31

PROVEAN

Benign

2.6

N;.

REVEL

Benign

0.052

Sift

Benign

1.0

T;.

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;.

Vest4

0.052

MPC

0.087

ClinPred

0.0081

GERP RS

2.6

Varity_R

0.025

gMVP

0.042

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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