chr12-52430567-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PS1_ModerateBP4_StrongBP6_ModerateBS2
The NM_004693.3(KRT75):c.1009G>A(p.Glu337Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00984 in 1,614,128 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_004693.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT75 | NM_004693.3 | c.1009G>A | p.Glu337Lys | missense_variant | 5/9 | ENST00000252245.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT75 | ENST00000252245.6 | c.1009G>A | p.Glu337Lys | missense_variant | 5/9 | 1 | NM_004693.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00646 AC: 983AN: 152178Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00740 AC: 1860AN: 251496Hom.: 14 AF XY: 0.00794 AC XY: 1079AN XY: 135922
GnomAD4 exome AF: 0.0102 AC: 14900AN: 1461832Hom.: 104 Cov.: 35 AF XY: 0.0102 AC XY: 7389AN XY: 727222
GnomAD4 genome ? AF: 0.00645 AC: 983AN: 152296Hom.: 5 Cov.: 33 AF XY: 0.00627 AC XY: 467AN XY: 74458
ClinVar
Submissions by phenotype
KRT75-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at