9-38396067-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000692.5(ALDH1B1):c.319C>T(p.Arg107Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R107L) has been classified as Likely benign.
Frequency
Consequence
NM_000692.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH1B1 | NM_000692.5 | c.319C>T | p.Arg107Cys | missense_variant | 2/2 | ENST00000377698.4 | NP_000683.3 | |
ALDH1B1 | XM_011517802.3 | c.460C>T | p.Arg154Cys | missense_variant | 2/2 | XP_011516104.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALDH1B1 | ENST00000377698.4 | c.319C>T | p.Arg107Cys | missense_variant | 2/2 | 1 | NM_000692.5 | ENSP00000366927.3 | ||
ALDH1B1 | ENST00000635162.1 | c.319C>T | p.Arg107Cys | missense_variant | 3/3 | 3 | ENSP00000489053.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251246Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135802
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461808Hom.: 0 Cov.: 100 AF XY: 0.0000206 AC XY: 15AN XY: 727202
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Uncertain significance and reported on 04-21-2015 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at