chr1-201283738-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001005337.3(PKP1):c.36C>T(p.Tyr12Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,613,826 control chromosomes in the GnomAD database, including 11,496 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001005337.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKP1 | NM_001005337.3 | c.36C>T | p.Tyr12Tyr | synonymous_variant | Exon 1 of 14 | ENST00000367324.8 | NP_001005337.1 | |
PKP1 | NM_000299.4 | c.36C>T | p.Tyr12Tyr | synonymous_variant | Exon 1 of 15 | NP_000290.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKP1 | ENST00000367324.8 | c.36C>T | p.Tyr12Tyr | synonymous_variant | Exon 1 of 14 | 1 | NM_001005337.3 | ENSP00000356293.4 | ||
PKP1 | ENST00000263946.7 | c.36C>T | p.Tyr12Tyr | synonymous_variant | Exon 1 of 15 | 5 | ENSP00000263946.3 | |||
PKP1 | ENST00000352845.3 | c.36C>T | p.Tyr12Tyr | synonymous_variant | Exon 1 of 14 | 5 | ENSP00000295597.3 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 25052AN: 152068Hom.: 2952 Cov.: 33
GnomAD3 exomes AF: 0.116 AC: 29039AN: 250988Hom.: 2310 AF XY: 0.113 AC XY: 15321AN XY: 135746
GnomAD4 exome AF: 0.0975 AC: 142472AN: 1461640Hom.: 8539 Cov.: 33 AF XY: 0.0983 AC XY: 71494AN XY: 727130
GnomAD4 genome AF: 0.165 AC: 25072AN: 152186Hom.: 2957 Cov.: 33 AF XY: 0.164 AC XY: 12221AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
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Epidermolysis bullosa simplex due to plakophilin deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at