12-52645039-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BP6BS2
The ENST00000309680.4(KRT2):c.1900G>A(p.Val634Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,614,074 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000309680.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT2 | NM_000423.3 | c.1900G>A | p.Val634Met | missense_variant | 9/9 | ENST00000309680.4 | NP_000414.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT2 | ENST00000309680.4 | c.1900G>A | p.Val634Met | missense_variant | 9/9 | 1 | NM_000423.3 | ENSP00000310861 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251336Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135852
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461868Hom.: 2 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 727238
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74408
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.1900G>A (p.V634M) alteration is located in exon 9 (coding exon 9) of the KRT2 gene. This alteration results from a G to A substitution at nucleotide position 1900, causing the valine (V) at amino acid position 634 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 15, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at