17-1270814-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_001164405.2(BHLHA9):c.251C>T(p.Ala84Val) variant causes a missense change. The variant allele was found at a frequency of 0.000129 in 1,475,800 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A84G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164405.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 151778Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000738 AC: 6AN: 81270Hom.: 0 AF XY: 0.0000862 AC XY: 4AN XY: 46382
GnomAD4 exome AF: 0.000128 AC: 169AN: 1324022Hom.: 1 Cov.: 32 AF XY: 0.000138 AC XY: 90AN XY: 652910
GnomAD4 genome AF: 0.000138 AC: 21AN: 151778Hom.: 0 Cov.: 33 AF XY: 0.0000810 AC XY: 6AN XY: 74118
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at