17-12894940-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000379672.10(ARHGAP44):c.54G>A(p.Arg18=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.00000694 in 1,585,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000379672.10 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP44 | NM_014859.6 | c.54G>A | p.Arg18= | splice_region_variant, synonymous_variant | 2/21 | ENST00000379672.10 | NP_055674.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP44 | ENST00000379672.10 | c.54G>A | p.Arg18= | splice_region_variant, synonymous_variant | 2/21 | 1 | NM_014859.6 | ENSP00000368994 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000628 AC: 9AN: 1433426Hom.: 0 Cov.: 30 AF XY: 0.00000986 AC XY: 7AN XY: 709918
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74196
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at