2-157799450-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001111067.4(ACVR1):c.44C>G(p.Ala15Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00858 in 1,611,556 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001111067.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00673 AC: 1019AN: 151476Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.0104 AC: 2610AN: 251244Hom.: 50 AF XY: 0.0125 AC XY: 1696AN XY: 135764
GnomAD4 exome AF: 0.00877 AC: 12803AN: 1459998Hom.: 168 Cov.: 31 AF XY: 0.00992 AC XY: 7209AN XY: 726428
GnomAD4 genome AF: 0.00673 AC: 1020AN: 151558Hom.: 9 Cov.: 32 AF XY: 0.00708 AC XY: 524AN XY: 74044
ClinVar
Submissions by phenotype
not provided Benign:4
ACVR1: BS1, BS2 -
- -
- -
See Variant Classification Assertion Criteria. -
not specified Benign:2
- -
- -
Progressive myositis ossificans Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at