rs2294039
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014629.4(ARHGEF10):c.2098G>A(p.Val700Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 1,614,074 control chromosomes in the GnomAD database, including 1,272 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014629.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF10 | NM_014629.4 | c.2098G>A | p.Val700Ile | missense_variant | 18/29 | ENST00000349830.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF10 | ENST00000349830.8 | c.2098G>A | p.Val700Ile | missense_variant | 18/29 | 1 | NM_014629.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0306 AC: 4663AN: 152198Hom.: 77 Cov.: 33
GnomAD3 exomes AF: 0.0315 AC: 7915AN: 251342Hom.: 152 AF XY: 0.0324 AC XY: 4403AN XY: 135904
GnomAD4 exome AF: 0.0383 AC: 56039AN: 1461758Hom.: 1195 Cov.: 65 AF XY: 0.0382 AC XY: 27775AN XY: 727190
GnomAD4 genome ? AF: 0.0306 AC: 4668AN: 152316Hom.: 77 Cov.: 33 AF XY: 0.0309 AC XY: 2298AN XY: 74478
ClinVar
Submissions by phenotype
Autosomal dominant slowed nerve conduction velocity Benign:3
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jan 15, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
ARHGEF10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at