rs2074225
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006725.5(CD6):c.770C>T(p.Ala257Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,545,390 control chromosomes in the GnomAD database, including 258,994 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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 benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. A257A) has been classified as Benign.
Frequency
Consequence
NM_006725.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD6 | NM_006725.5 | c.770C>T | p.Ala257Val | missense_variant | 4/13 | ENST00000313421.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD6 | ENST00000313421.11 | c.770C>T | p.Ala257Val | missense_variant | 4/13 | 1 | NM_006725.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.578 AC: 87928AN: 152034Hom.: 25897 Cov.: 34
GnomAD3 exomes AF: 0.535 AC: 103323AN: 193210Hom.: 28403 AF XY: 0.541 AC XY: 56298AN XY: 104034
GnomAD4 exome AF: 0.575 AC: 800477AN: 1393238Hom.: 233083 Cov.: 46 AF XY: 0.574 AC XY: 392418AN XY: 683970
GnomAD4 genome ? AF: 0.578 AC: 87977AN: 152152Hom.: 25911 Cov.: 34 AF XY: 0.568 AC XY: 42229AN XY: 74376
ClinVar
Submissions by phenotype
CD6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 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