12-52469245-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_173086.5(KRT6C):c.1512C>T(p.Gly504=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
KRT6C
NM_173086.5 synonymous
NM_173086.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.464
Genes affected
KRT6C (HGNC:20406): (keratin 6C) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. The type II keratins are clustered in a region of chromosome 12q13. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 12-52469245-G-A is Benign according to our data. Variant chr12-52469245-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681361.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.464 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| KRT6C | NM_173086.5 | c.1512C>T | p.Gly504= | synonymous_variant | 9/9 | ENST00000252250.7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KRT6C | ENST00000252250.7 | c.1512C>T | p.Gly504= | synonymous_variant | 9/9 | 1 | NM_173086.5 | P1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461596Hom.: 0 Cov.: 37 AF XY: 0.00000138 AC XY: 1AN XY: 727080
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GnomAD4 genome 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
EBV-positive nodal T- and NK-cell lymphoma Benign:1
| Likely benign, no assertion criteria provided | research | Department of Clinical Pathology, School of Medicine, Fujita Health University | - | - - |
Computational scores
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at