chrX-131088720-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_144967.4(ARHGAP36):c.1579C>T(p.Arg527Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,711 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R527S) has been classified as Uncertain significance.
Frequency
Consequence
NM_144967.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP36 | NM_144967.4 | c.1579C>T | p.Arg527Cys | missense_variant | 12/12 | ENST00000276211.10 | |
ARHGAP36 | NM_001282607.2 | c.1543C>T | p.Arg515Cys | missense_variant | 12/12 | ||
ARHGAP36 | NM_001330651.1 | c.1171C>T | p.Arg391Cys | missense_variant | 11/11 | ||
ARHGAP36 | XM_011531280.2 | c.1171C>T | p.Arg391Cys | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP36 | ENST00000276211.10 | c.1579C>T | p.Arg527Cys | missense_variant | 12/12 | 2 | NM_144967.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000549 AC: 1AN: 182217Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66709
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097711Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 363081
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | ARHGAP36: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at