chr5-143121118-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001135608.3(ARHGAP26):c.1669A>G(p.Ile557Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,613,784 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_001135608.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP26 | NM_001135608.3 | c.1669A>G | p.Ile557Val | missense_variant | 18/23 | ENST00000645722.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP26 | ENST00000645722.2 | c.1669A>G | p.Ile557Val | missense_variant | 18/23 | NM_001135608.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 170AN: 152254Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000307 AC: 77AN: 250882Hom.: 1 AF XY: 0.000221 AC XY: 30AN XY: 135580
GnomAD4 exome AF: 0.000115 AC: 168AN: 1461412Hom.: 1 Cov.: 30 AF XY: 0.000100 AC XY: 73AN XY: 727002
GnomAD4 genome ? AF: 0.00112 AC: 170AN: 152372Hom.: 1 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74512
ClinVar
Submissions by phenotype
ARHGAP26-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at