Variant 17-41525223-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002276.5(KRT19):c.471T>C(p.Asn157=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 1,612,236 control chromosomes in the GnomAD database, including 344,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.65 ( 32279 hom., cov: 32)

Exomes 𝑓: 0.65 ( 312525 hom. )

Consequence

KRT19
NM_002276.5 synonymous

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.146

Variant links:

Genes affected

KRT19 (HGNC:6436): (keratin 19) The protein encoded by this gene is a member of the keratin family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. The type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains. Unlike its related family members, this smallest known acidic cytokeratin is not paired with a basic cytokeratin in epithelial cells. It is specifically expressed in the periderm, the transiently superficial layer that envelopes the developing epidermis. The type I cytokeratins are clustered in a region of chromosome 17q12-q21. [provided by RefSeq, Jul 2008]

KRT19 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=0.146 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRT19	NM_002276.5 linkuse as main transcript	c.471T>C	p.Asn157=	synonymous_variant	2/6	ENST00000361566.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT19	ENST00000361566.7 linkuse as main transcript	c.471T>C	p.Asn157=	synonymous_variant	2/6	1	NM_002276.5	P1

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98433

AN:

151954

Hom.:

32250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.685

Gnomad AMR

AF:

0.750

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.633

Gnomad OTH

AF:

0.662

GnomAD3 exomes

AF:

0.691

AC:

173814

AN:

251466

Hom.:

61211

AF XY:

0.692

AC XY:

94077

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.583

Gnomad AMR exome

AF:

0.787

Gnomad ASJ exome

AF:

0.661

Gnomad EAS exome

AF:

0.916

Gnomad SAS exome

AF:

0.762

Gnomad FIN exome

AF:

0.636

Gnomad NFE exome

AF:

0.635

Gnomad OTH exome

AF:

0.690

GnomAD4 exome

AF:

0.650

AC:

949807

AN:

1460164

Hom.:

312525

Cov.:

AF XY:

0.654

AC XY:

474874

AN XY:

726460

show subpopulations

Gnomad4 AFR exome

AF:

0.580

Gnomad4 AMR exome

AF:

0.783

Gnomad4 ASJ exome

AF:

0.660

Gnomad4 EAS exome

AF:

0.932

Gnomad4 SAS exome

AF:

0.757

Gnomad4 FIN exome

AF:

0.643

Gnomad4 NFE exome

AF:

0.628

Gnomad4 OTH exome

AF:

0.657

GnomAD4 genome

AF:

0.648

AC:

98510

AN:

152072

Hom.:

32279

Cov.:

AF XY:

0.654

AC XY:

48599

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.587

Gnomad4 AMR

AF:

0.751

Gnomad4 ASJ

AF:

0.673

Gnomad4 EAS

AF:

0.917

Gnomad4 SAS

AF:

0.771

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.633

Gnomad4 OTH

AF:

0.667

Alfa

AF:

0.617

Hom.:

10946

Bravo

AF:

0.651

Asia WGS

AF:

0.825

AC:

2868

AN:

3478

EpiCase

AF:

0.644

EpiControl

AF:

0.648

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

not provided, no classification provided

literature only

Epithelial Biology; Institute of Medical Biology, Singapore

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

5.7

DANN

Benign

0.65

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