dbSNP rs769193911: KRTAP4-7:p.Gln101Gln (chr17-41084509-G-A) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_033061.4(KRTAP4-7):c.303G>A(p.Gln101Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 125,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 25)

Exomes 𝑓: 0.00078 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

KRTAP4-7
NM_033061.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.49

Variant links:

Genes affected

KRTAP4-7 (HGNC:18898): (keratin associated protein 4-7) This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the ultrahigh sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Mar 2009]

KRTAP4-7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP7

Synonymous conserved (PhyloP=-3.49 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTAP4-7	NM_033061.4 link	c.303G>A	p.Gln101Gln	synonymous_variant	Exon 1 of 1	ENST00000391417.6	NP_149050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTAP4-7	ENST00000391417.6 link	c.303G>A	p.Gln101Gln	synonymous_variant	Exon 1 of 1	6	NM_033061.4	ENSP00000375236.4		Q9BYR0

Frequencies

GnomAD3 genomes

AF:

0.00117

AC:

147

AN:

125762

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00115

Gnomad AMI

AF:

0.00139

Gnomad AMR

AF:

0.000935

Gnomad ASJ

AF:

0.00207

Gnomad EAS

AF:

0.00131

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00214

Gnomad MID

AF:

0.00472

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.000591

GnomAD3 exomes

AF:

0.000545

AC:

126

AN:

231074

Hom.:

AF XY:

0.000443

AC XY:

AN XY:

126372

show subpopulations

Gnomad AFR exome

AF:

0.00132

Gnomad AMR exome

AF:

0.000510

Gnomad ASJ exome

AF:

0.000317

Gnomad EAS exome

AF:

0.000884

Gnomad SAS exome

AF:

0.000413

Gnomad FIN exome

AF:

0.0000949

Gnomad NFE exome

AF:

0.000544

Gnomad OTH exome

AF:

0.000730

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000780

AC:

1111

AN:

1424612

Hom.:

Cov.:

137

AF XY:

0.000786

AC XY:

557

AN XY:

708572

show subpopulations

Gnomad4 AFR exome

AF:

0.00113

Gnomad4 AMR exome

AF:

0.00151

Gnomad4 ASJ exome

AF:

0.00231

Gnomad4 EAS exome

AF:

0.00119

Gnomad4 SAS exome

AF:

0.000453

Gnomad4 FIN exome

AF:

0.00143

Gnomad4 NFE exome

AF:

0.000658

Gnomad4 OTH exome

AF:

0.00119

GnomAD4 genome

AF:

0.00117

AC:

147

AN:

125888

Hom.:

Cov.:

AF XY:

0.00107

AC XY:

AN XY:

61506

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.000934

Gnomad4 ASJ

AF:

0.00207

Gnomad4 EAS

AF:

0.00131

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00214

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.000583

Alfa

AF:

0.000257

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.32

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over