4-99347074-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000669.5(ADH1C):c.191T>C(p.Val64Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000669.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADH1C | NM_000669.5 | c.191T>C | p.Val64Ala | missense_variant | 3/9 | ENST00000515683.6 | |
ADH1C | NR_133005.2 | n.262T>C | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADH1C | ENST00000515683.6 | c.191T>C | p.Val64Ala | missense_variant | 3/9 | 1 | NM_000669.5 | P1 | |
ADH1C | ENST00000510055.5 | c.71T>C | p.Val24Ala | missense_variant | 4/7 | 3 | |||
ADH1C | ENST00000511397.3 | c.89T>C | p.Val30Ala | missense_variant | 2/5 | 3 | |||
ADH1C | ENST00000505942.2 | n.260T>C | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251412Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135880
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727230
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at