GeneBe

rs1894035

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000548657.5(KRT7):​n.423T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

KRT7
ENST00000548657.5 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

Publications

8 publications found
Variant links:
Genes affected
KRT7 (HGNC:6445): (keratin 7) 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 simple epithelia lining the cavities of the internal organs and in the gland ducts and blood vessels. The genes encoding the type II cytokeratins are clustered in a region of chromosome 12q12-q13. Alternative splicing may result in several transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]
KRT86 (HGNC:6463): (keratin 86) This gene encodes a type II keratin protein, which heterodimerizes with type I keratins to form hair and nails. This gene is present in a cluster of related genes and pseudogenes on chromosome 12. Mutations in this gene have been observed in patients with the hair disease monilethrix. [provided by RefSeq, Feb 2016]
KRT87P (HGNC:30198): (keratin 87, pseudogene) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT7XM_011538325.3 linkc.*61T>A 3_prime_UTR_variant Exon 8 of 8 XP_011536627.1
KRT87PNR_146088.1 linkn.1243+57A>T intron_variant Intron 8 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT7ENST00000548657.5 linkn.423T>A non_coding_transcript_exon_variant Exon 3 of 3 3
KRT86ENST00000553310.6 linkc.-5+2542T>A intron_variant Intron 1 of 2 4 ENSP00000452237.3 U3KPR1
KRT87PENST00000529785.1 linkn.1602+57A>T intron_variant Intron 8 of 8 2
KRT87PENST00000534226.5 linkn.1288+57A>T intron_variant Intron 8 of 8 6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
447664
Hom.:
0
Cov.:
3
AF XY:
0.00
AC XY:
0
AN XY:
245092
African (AFR)
AF:
0.00
AC:
0
AN:
13408
American (AMR)
AF:
0.00
AC:
0
AN:
31178
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16708
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22094
South Asian (SAS)
AF:
0.00
AC:
0
AN:
60870
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
22268
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3578
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
253458
Other (OTH)
AF:
0.00
AC:
0
AN:
24102
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
9690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
4.0
DANN
Benign
0.80
PhyloP100
0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1894035; hg19: chr12-52645754; API