rs11230562
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006725.5(CD6):c.650C>T(p.Thr217Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,606,434 control chromosomes in the GnomAD database, including 38,470 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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.
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.650C>T | p.Thr217Met | missense_variant | 4/13 | ENST00000313421.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD6 | ENST00000313421.11 | c.650C>T | p.Thr217Met | missense_variant | 4/13 | 1 | NM_006725.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.159 AC: 24160AN: 152160Hom.: 2685 Cov.: 34
GnomAD3 exomes AF: 0.171 AC: 39518AN: 230678Hom.: 4445 AF XY: 0.174 AC XY: 21892AN XY: 125964
GnomAD4 exome AF: 0.211 AC: 306953AN: 1454156Hom.: 35785 Cov.: 46 AF XY: 0.209 AC XY: 151022AN XY: 722760
GnomAD4 genome AF: 0.159 AC: 24145AN: 152278Hom.: 2685 Cov.: 34 AF XY: 0.155 AC XY: 11576AN XY: 74460
ClinVar
Submissions by phenotype
CD6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 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