9-38396068-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000692.5(ALDH1B1):c.320G>T(p.Arg107Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,613,740 control chromosomes in the GnomAD database, including 262,050 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R107C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000692.5 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 |
---|---|---|---|---|---|---|---|
ALDH1B1 | NM_000692.5 | c.320G>T | p.Arg107Leu | missense_variant | 2/2 | ENST00000377698.4 | |
ALDH1B1 | XM_011517802.3 | c.461G>T | p.Arg154Leu | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1B1 | ENST00000377698.4 | c.320G>T | p.Arg107Leu | missense_variant | 2/2 | 1 | NM_000692.5 | P1 | |
ALDH1B1 | ENST00000635162.1 | c.320G>T | p.Arg107Leu | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.488 AC: 74167AN: 151934Hom.: 19573 Cov.: 33
GnomAD3 exomes AF: 0.510 AC: 128169AN: 251134Hom.: 34962 AF XY: 0.529 AC XY: 71746AN XY: 135748
GnomAD4 exome AF: 0.570 AC: 832672AN: 1461688Hom.: 242478 Cov.: 95 AF XY: 0.572 AC XY: 416098AN XY: 727114
GnomAD4 genome AF: 0.488 AC: 74190AN: 152052Hom.: 19572 Cov.: 33 AF XY: 0.484 AC XY: 35965AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 05, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at