rs17683288
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014629.4(ARHGEF10):āc.2950T>Gā(p.Ser984Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 1,613,890 control chromosomes in the GnomAD database, including 3,648 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 (ā ā ).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF10 | NM_014629.4 | c.2950T>G | p.Ser984Ala | missense_variant | 25/29 | ENST00000349830.8 | NP_055444.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF10 | ENST00000349830.8 | c.2950T>G | p.Ser984Ala | missense_variant | 25/29 | 1 | NM_014629.4 | ENSP00000340297 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0504 AC: 7674AN: 152202Hom.: 265 Cov.: 33
GnomAD3 exomes AF: 0.0545 AC: 13694AN: 251466Hom.: 461 AF XY: 0.0560 AC XY: 7613AN XY: 135908
GnomAD4 exome AF: 0.0647 AC: 94603AN: 1461570Hom.: 3383 Cov.: 32 AF XY: 0.0648 AC XY: 47116AN XY: 727112
GnomAD4 genome AF: 0.0504 AC: 7676AN: 152320Hom.: 265 Cov.: 33 AF XY: 0.0505 AC XY: 3762AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
ARHGEF10-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 30, 2024 | 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