Genetic Variant KRT5:c.*185G>A (chr12-52514757-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_000424.4(KRT5):c.*185G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 617,116 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 90 hom., cov: 31)

Exomes 𝑓: 0.011 ( 104 hom. )

Consequence

KRT5
NM_000424.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.31

Variant links:

Genes affected

KRT5 (HGNC:6442): (keratin 5) 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 basal layer of the epidermis with family member KRT14. Mutations in these genes have been associated with a complex of diseases termed epidermolysis bullosa simplex. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]

KRT5 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=-0.91).

BP6

Variant 12-52514757-C-T is Benign according to our data. Variant chr12-52514757-C-T is described in ClinVar as [Benign]. Clinvar id is 309551.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT5	NM_000424.4 link	c.*185G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000252242.9	NP_000415.2	P13647

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT5	ENST00000252242 link	c.*185G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_000424.4	ENSP00000252242.4		P13647
KRT5	ENST00000552952.1 link	n.*239G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0229

AC:

3477

AN:

151958

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0510

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.0500

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.0303

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.000567

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00463

Gnomad OTH

AF:

0.0278

GnomAD4 exome

AF:

0.0106

AC:

4914

AN:

465040

Hom.:

104

Cov.:

AF XY:

0.0102

AC XY:

2490

AN XY:

244986

show subpopulations

Gnomad4 AFR exome

AF:

0.0534

Gnomad4 AMR exome

AF:

0.0618

Gnomad4 ASJ exome

AF:

0.000502

Gnomad4 EAS exome

AF:

0.0220

Gnomad4 SAS exome

AF:

0.0105

Gnomad4 FIN exome

AF:

0.000357

Gnomad4 NFE exome

AF:

0.00491

Gnomad4 OTH exome

AF:

0.0147

GnomAD4 genome

AF:

0.0230

AC:

3499

AN:

152076

Hom.:

Cov.:

AF XY:

0.0238

AC XY:

1770

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0514

Gnomad4 AMR

AF:

0.0502

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.0300

Gnomad4 SAS

AF:

0.0131

Gnomad4 FIN

AF:

0.000567

Gnomad4 NFE

AF:

0.00463

Gnomad4 OTH

AF:

0.0270

Alfa

AF:

0.00242

Hom.:

Bravo

AF:

0.0277

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Epidermolysis bullosa simplex

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.92

DANN

Benign

0.41

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