Variant 17-41583206-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000526.5(KRT14):c.1274+29C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 1,613,036 control chromosomes in the GnomAD database, including 1,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 157 hom., cov: 32)

Exomes 𝑓: 0.032 ( 1655 hom. )

Consequence

KRT14
NM_000526.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.58

Variant links:

Genes affected

KRT14 (HGNC:6416): (keratin 14) This gene encodes a member of the keratin family, the most diverse group of intermediate filaments. This gene product, a type I keratin, is usually found as a heterotetramer with two keratin 5 molecules, a type II keratin. Together they form the cytoskeleton of epithelial cells. Mutations in the genes for these keratins are associated with epidermolysis bullosa simplex. At least one pseudogene has been identified at 17p12-p11. [provided by RefSeq, Jul 2008]

KRT14 links:

KRT14 (HGNC:):

KRT14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-41583206-G-C is Benign according to our data. Variant chr17-41583206-G-C is described in ClinVar as [Benign]. Clinvar id is 1271599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRT14	NM_000526.5 linkuse as main transcript	c.1274+29C>G		intron_variant		ENST00000167586.7	NP_000517.3	P02533

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
KRT14	ENST00000167586.7 linkuse as main transcript	c.1274+29C>G	intron_variant	1	NM_000526.5	ENSP00000167586.6	P02533
KRT14	ENST00000441550.2 linkuse as main transcript	n.221+29C>G	intron_variant	2
KRT14	ENST00000476662.1 linkuse as main transcript	n.*43C>G	downstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0254

AC:

3861

AN:

152032

Hom.:

157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00556

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.0588

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.00961

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0311

GnomAD3 exomes

AF:

0.0439

AC:

11008

AN:

250964

Hom.:

623

AF XY:

0.0478

AC XY:

6487

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.00552

Gnomad AMR exome

AF:

0.0135

Gnomad ASJ exome

AF:

0.0595

Gnomad EAS exome

AF:

0.175

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0108

Gnomad NFE exome

AF:

0.0222

Gnomad OTH exome

AF:

0.0368

GnomAD4 exome

AF:

0.0317

AC:

46308

AN:

1460886

Hom.:

1655

Cov.:

AF XY:

0.0344

AC XY:

25017

AN XY:

726760

show subpopulations

Gnomad4 AFR exome

AF:

0.00521

Gnomad4 AMR exome

AF:

0.0148

Gnomad4 ASJ exome

AF:

0.0589

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.0106

Gnomad4 NFE exome

AF:

0.0219

Gnomad4 OTH exome

AF:

0.0418

GnomAD4 genome

AF:

0.0254

AC:

3864

AN:

152150

Hom.:

157

Cov.:

AF XY:

0.0265

AC XY:

1968

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.00559

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.0588

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.00961

Gnomad4 NFE

AF:

0.0217

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0156

Hom.:

Bravo

AF:

0.0241

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.50

DANN

Benign

0.48

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