rs139659618
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_020754.4(ARHGAP31):c.2344C>A(p.Pro782Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,614,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020754.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP31 | NM_020754.4 | c.2344C>A | p.Pro782Thr | missense_variant | 12/12 | ENST00000264245.9 | NP_065805.2 | |
ARHGAP31 | XM_006713714.4 | c.2284C>A | p.Pro762Thr | missense_variant | 12/12 | XP_006713777.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP31 | ENST00000264245.9 | c.2344C>A | p.Pro782Thr | missense_variant | 12/12 | 1 | NM_020754.4 | ENSP00000264245.4 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 223AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000425 AC: 106AN: 249188Hom.: 0 AF XY: 0.000385 AC XY: 52AN XY: 135170
GnomAD4 exome AF: 0.000182 AC: 266AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.000182 AC XY: 132AN XY: 727244
GnomAD4 genome AF: 0.00147 AC: 224AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.00165 AC XY: 123AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 28, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 09, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2020 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 11, 2016 | - - |
ARHGAP31-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 04, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2024 | 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