rs17229382
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001256106.3(CD101):c.2515G>A(p.Val839Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0179 in 1,613,910 control chromosomes in the GnomAD database, including 338 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001256106.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD101 | NM_001256106.3 | c.2515G>A | p.Val839Ile | missense_variant | 8/10 | ENST00000682167.1 | |
CD101-AS1 | NR_110786.1 | n.1701C>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD101 | ENST00000682167.1 | c.2515G>A | p.Val839Ile | missense_variant | 8/10 | NM_001256106.3 | P1 | ||
CD101 | ENST00000369470.1 | c.2515G>A | p.Val839Ile | missense_variant | 8/10 | 1 | P1 | ||
CD101-AS1 | ENST00000445523.1 | n.1701C>T | non_coding_transcript_exon_variant | 4/4 | 2 | ||||
CD101 | ENST00000256652.8 | c.2515G>A | p.Val839Ile | missense_variant | 8/9 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0143 AC: 2184AN: 152222Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.0177 AC: 4448AN: 250864Hom.: 74 AF XY: 0.0163 AC XY: 2206AN XY: 135572
GnomAD4 exome AF: 0.0183 AC: 26718AN: 1461570Hom.: 307 Cov.: 31 AF XY: 0.0177 AC XY: 12849AN XY: 727088
GnomAD4 genome ? AF: 0.0143 AC: 2182AN: 152340Hom.: 31 Cov.: 32 AF XY: 0.0152 AC XY: 1132AN XY: 74488
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at