rs10489990
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_015717.5(CD207):c.164C>T(p.Ala55Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,612,328 control chromosomes in the GnomAD database, including 96,343 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_015717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD207 | NM_015717.5 | c.164C>T | p.Ala55Val | missense_variant | 2/6 | ENST00000410009.5 | NP_056532.4 | |
CD207 | XM_011532875.3 | c.164C>T | p.Ala55Val | missense_variant | 2/7 | XP_011531177.1 | ||
CD207 | XM_011532876.3 | c.164C>T | p.Ala55Val | missense_variant | 2/6 | XP_011531178.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.298 AC: 45249AN: 151978Hom.: 7371 Cov.: 32
GnomAD3 exomes AF: 0.333 AC: 82843AN: 248744Hom.: 14335 AF XY: 0.334 AC XY: 45008AN XY: 134944
GnomAD4 exome AF: 0.346 AC: 504847AN: 1460232Hom.: 88964 Cov.: 35 AF XY: 0.344 AC XY: 250108AN XY: 726450
GnomAD4 genome AF: 0.298 AC: 45269AN: 152096Hom.: 7379 Cov.: 32 AF XY: 0.297 AC XY: 22085AN XY: 74362
ClinVar
Submissions by phenotype
CD207-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 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