Variant 12-52790835-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_057088.3(KRT3):c.1570+2dupT variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.074 in 1,594,442 control chromosomes in the GnomAD database, including 4,912 homozygotes. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.059 ( 345 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4567 hom. )

Consequence

KRT3
NM_057088.3 splice_donor, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.69

Variant links:

Genes affected

KRT3 (HGNC:6440): (keratin 3) The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the corneal epithelium with family member KRT12 and mutations in these genes have been associated with Meesmann's Corneal Dystrophy. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]

KRT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-52790835-T-TA is Benign according to our data. Variant chr12-52790835-T-TA is described in ClinVar as [Benign]. Clinvar id is 2033335.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRT3	NM_057088.3 link	c.1570+2dupT		splice_donor_variant, intron_variant		ENST00000417996.2	NP_476429.2	P12035

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRT3	ENST00000417996.2 link	c.1570+2dupT		splice_donor_variant, intron_variant		1	NM_057088.3	ENSP00000413479.2		P12035

Frequencies

GnomAD3 genomes

AF:

0.0594

AC:

9047

AN:

152228

Hom.:

345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0155

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0708

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0443

Gnomad FIN

AF:

0.0511

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0859

Gnomad OTH

AF:

0.0736

GnomAD3 exomes

AF:

0.0624

AC:

13838

AN:

221852

Hom.:

574

AF XY:

0.0637

AC XY:

7583

AN XY:

119066

show subpopulations

Gnomad AFR exome

AF:

0.0128

Gnomad AMR exome

AF:

0.0440

Gnomad ASJ exome

AF:

0.114

Gnomad EAS exome

AF:

0.000244

Gnomad SAS exome

AF:

0.0485

Gnomad FIN exome

AF:

0.0575

Gnomad NFE exome

AF:

0.0839

Gnomad OTH exome

AF:

0.0802

GnomAD4 exome

AF:

0.0755

AC:

108920

AN:

1442096

Hom.:

4567

Cov.:

AF XY:

0.0754

AC XY:

53925

AN XY:

715260

show subpopulations

Gnomad4 AFR exome

AF:

0.0124

Gnomad4 AMR exome

AF:

0.0480

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.000179

Gnomad4 SAS exome

AF:

0.0502

Gnomad4 FIN exome

AF:

0.0604

Gnomad4 NFE exome

AF:

0.0827

Gnomad4 OTH exome

AF:

0.0738

GnomAD4 genome

AF:

0.0594

AC:

9045

AN:

152346

Hom.:

345

Cov.:

AF XY:

0.0575

AC XY:

4285

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0155

Gnomad4 AMR

AF:

0.0707

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0439

Gnomad4 FIN

AF:

0.0511

Gnomad4 NFE

AF:

0.0859

Gnomad4 OTH

AF:

0.0733

Alfa

AF:

0.0599

Hom.:

Bravo

AF:

0.0599

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.89

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.89

Position offset: 3

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