Variant 12-52898449-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002273.4(KRT8):c.1261+11delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 1,612,462 control chromosomes in the GnomAD database, including 1,009 homozygotes. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.024 ( 73 hom., cov: 32)

Exomes 𝑓: 0.032 ( 936 hom. )

Consequence

KRT8
NM_002273.4 intron

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.826

Variant links:

Genes affected

KRT8 (HGNC:6446): (keratin 8) This gene is a member of the type II keratin family clustered on the long arm of chromosome 12. Type I and type II keratins heteropolymerize to form intermediate-sized filaments in the cytoplasm of epithelial cells. The product of this gene typically dimerizes with keratin 18 to form an intermediate filament in simple single-layered epithelial cells. This protein plays a role in maintaining cellular structural integrity and also functions in signal transduction and cellular differentiation. Mutations in this gene cause cryptogenic cirrhosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

KRT8 links:

KRT8 (HGNC:):

KRT8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
KRT8	NM_002273.4 linkuse as main transcript	c.1261+11delC	intron_variant	ENST00000692008.1	NP_002264.1	P05787-1
KRT8	NM_001256282.2 linkuse as main transcript	c.1345+11delC	intron_variant		NP_001243211.1	Q7L4M3
KRT8	NM_001256293.2 linkuse as main transcript	c.1261+11delC	intron_variant		NP_001243222.1	P05787-1
KRT8	NR_045962.2 linkuse as main transcript	n.1712+11delC	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRT8	ENST00000692008.1 linkuse as main transcript	c.1261+11delC		intron_variant			NM_002273.4	ENSP00000509398.1		P05787-1

Frequencies

GnomAD3 genomes

AF:

0.0235

AC:

3572

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00845

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0515

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.0137

Gnomad SAS

AF:

0.0401

Gnomad FIN

AF:

0.0160

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0284

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.0349

AC:

8659

AN:

247864

Hom.:

263

AF XY:

0.0336

AC XY:

4509

AN XY:

134316

show subpopulations

Gnomad AFR exome

AF:

0.00704

Gnomad AMR exome

AF:

0.0972

Gnomad ASJ exome

AF:

0.00311

Gnomad EAS exome

AF:

0.00897

Gnomad SAS exome

AF:

0.0495

Gnomad FIN exome

AF:

0.0173

Gnomad NFE exome

AF:

0.0266

Gnomad OTH exome

AF:

0.0308

GnomAD4 exome

AF:

0.0317

AC:

46313

AN:

1460244

Hom.:

936

Cov.:

AF XY:

0.0317

AC XY:

23009

AN XY:

726342

show subpopulations

Gnomad4 AFR exome

AF:

0.00532

Gnomad4 AMR exome

AF:

0.0906

Gnomad4 ASJ exome

AF:

0.00295

Gnomad4 EAS exome

AF:

0.0300

Gnomad4 SAS exome

AF:

0.0475

Gnomad4 FIN exome

AF:

0.0182

Gnomad4 NFE exome

AF:

0.0305

Gnomad4 OTH exome

AF:

0.0282

GnomAD4 genome

AF:

0.0236

AC:

3596

AN:

152218

Hom.:

Cov.:

AF XY:

0.0233

AC XY:

1732

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.00840

Gnomad4 AMR

AF:

0.0524

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.0138

Gnomad4 SAS

AF:

0.0402

Gnomad4 FIN

AF:

0.0160

Gnomad4 NFE

AF:

0.0284

Gnomad4 OTH

AF:

0.0236

Alfa

AF:

0.0236

Hom.:

Bravo

AF:

0.0259

Asia WGS

AF:

0.0350

AC:

122

AN:

3476

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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