chr12-52567039-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_175053.4(KRT74):c.1520G>T(p.Gly507Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,600,310 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_175053.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT74 | NM_175053.4 | c.1520G>T | p.Gly507Val | missense_variant | 9/9 | ENST00000305620.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT74 | ENST00000305620.3 | c.1520G>T | p.Gly507Val | missense_variant | 9/9 | 1 | NM_175053.4 | P1 | |
KRT74 | ENST00000549343.5 | c.1562G>T | p.Gly521Val | missense_variant | 10/10 | 5 | |||
KRT74 | ENST00000546384.1 | n.507G>T | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00139 AC: 211AN: 152086Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00111 AC: 267AN: 240856Hom.: 1 AF XY: 0.00102 AC XY: 133AN XY: 130172
GnomAD4 exome AF: 0.00185 AC: 2674AN: 1448106Hom.: 4 Cov.: 30 AF XY: 0.00176 AC XY: 1268AN XY: 718542
GnomAD4 genome ? AF: 0.00139 AC: 211AN: 152204Hom.: 2 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at