17-1270679-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001164405.2(BHLHA9):c.116C>A(p.Ala39Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000881 in 1,321,460 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001164405.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00443 AC: 673AN: 152054Hom.: 8 Cov.: 33
GnomAD4 exome AF: 0.000416 AC: 486AN: 1169298Hom.: 6 Cov.: 31 AF XY: 0.000345 AC XY: 195AN XY: 564690
GnomAD4 genome AF: 0.00446 AC: 678AN: 152162Hom.: 8 Cov.: 33 AF XY: 0.00394 AC XY: 293AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at