chr16-66469802-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001178020.3(BEAN1):c.226C>A(p.Arg76Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,535,802 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001178020.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00809 AC: 1230AN: 152002Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00775 AC: 1068AN: 137830Hom.: 8 AF XY: 0.00835 AC XY: 624AN XY: 74744
GnomAD4 exome AF: 0.0103 AC: 14219AN: 1383682Hom.: 100 Cov.: 32 AF XY: 0.0102 AC XY: 6956AN XY: 682786
GnomAD4 genome AF: 0.00809 AC: 1231AN: 152120Hom.: 9 Cov.: 32 AF XY: 0.00910 AC XY: 677AN XY: 74368
ClinVar
Submissions by phenotype
not provided Benign:1
BEAN1: BP4, BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at