12-52469127-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_173086.5(KRT6C):c.1630G>A(p.Gly544Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,614,054 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G544G) has been classified as Benign.
Frequency
Consequence
NM_173086.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT6C | NM_173086.5 | c.1630G>A | p.Gly544Ser | missense_variant | 9/9 | ENST00000252250.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT6C | ENST00000252250.7 | c.1630G>A | p.Gly544Ser | missense_variant | 9/9 | 1 | NM_173086.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000729 AC: 111AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251394Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135860
GnomAD4 exome AF: 0.000101 AC: 147AN: 1461732Hom.: 1 Cov.: 35 AF XY: 0.0000949 AC XY: 69AN XY: 727174
GnomAD4 genome AF: 0.000735 AC: 112AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74472
ClinVar
Submissions by phenotype
KRT6C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at