Variant chr11-1630317-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001001480.3(KRTAP5-5):c.477C>T(p.Cys159Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 1,580,376 control chromosomes in the GnomAD database, including 348 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.012 ( 199 hom., cov: 28)

Exomes 𝑓: 0.0050 ( 149 hom. )

Consequence

KRTAP5-5
NM_001001480.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.462

Variant links:

Genes affected

KRTAP5-5 (HGNC:23601): (keratin associated protein 5-5) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP5-5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 11-1630317-C-T is Benign according to our data. Variant chr11-1630317-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3234174.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.462 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0118 (1783/151036) while in subpopulation NFE AF= 0.0164 (1108/67544). AF 95% confidence interval is 0.0156. There are 199 homozygotes in gnomad4. There are 820 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 199 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-5	NM_001001480.3 linkuse as main transcript	c.477C>T	p.Cys159Cys	synonymous_variant	1/1	ENST00000399676.4	NP_001001480.2	Q701N2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-5	ENST00000399676.4 linkuse as main transcript	c.477C>T	p.Cys159Cys	synonymous_variant	1/1	6	NM_001001480.3	ENSP00000382584.2		Q701N2

Frequencies

GnomAD3 genomes

AF:

0.0118

AC:

1785

AN:

150920

Hom.:

199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00321

Gnomad AMI

AF:

0.0848

Gnomad AMR

AF:

0.00797

Gnomad ASJ

AF:

0.0576

Gnomad EAS

AF:

0.000775

Gnomad SAS

AF:

0.0119

Gnomad FIN

AF:

0.00689

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0164

Gnomad OTH

AF:

0.00673

GnomAD3 exomes

AF:

0.00370

AC:

909

AN:

245546

Hom.:

AF XY:

0.00345

AC XY:

458

AN XY:

132616

show subpopulations

Gnomad AFR exome

AF:

0.000821

Gnomad AMR exome

AF:

0.00151

Gnomad ASJ exome

AF:

0.0127

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00302

Gnomad FIN exome

AF:

0.00327

Gnomad NFE exome

AF:

0.00485

Gnomad OTH exome

AF:

0.00532

GnomAD4 exome

AF:

0.00505

AC:

7217

AN:

1429340

Hom.:

149

Cov.:

103

AF XY:

0.00554

AC XY:

3943

AN XY:

711666

show subpopulations

Gnomad4 AFR exome

AF:

0.000898

Gnomad4 AMR exome

AF:

0.00229

Gnomad4 ASJ exome

AF:

0.0314

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00936

Gnomad4 FIN exome

AF:

0.00608

Gnomad4 NFE exome

AF:

0.00435

Gnomad4 OTH exome

AF:

0.00779

GnomAD4 genome

AF:

0.0118

AC:

1783

AN:

151036

Hom.:

199

Cov.:

AF XY:

0.0111

AC XY:

820

AN XY:

73806

show subpopulations

Gnomad4 AFR

AF:

0.00320

Gnomad4 AMR

AF:

0.00796

Gnomad4 ASJ

AF:

0.0576

Gnomad4 EAS

AF:

0.000777

Gnomad4 SAS

AF:

0.0117

Gnomad4 FIN

AF:

0.00689

Gnomad4 NFE

AF:

0.0164

Gnomad4 OTH

AF:

0.00666

Alfa

AF:

0.0142

Hom.:

Bravo

AF:

0.0119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2024

KRTAP5-5: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

3.2

DANN

Benign

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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