chrX-131081798-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144967.4(ARHGAP36):c.133C>A(p.Arg45Ser) 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 1,098,243 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.133C>A | p.Arg45Ser | missense_variant | 2/12 | ENST00000276211.10 | |
ARHGAP36 | NM_001282607.2 | c.97C>A | p.Arg33Ser | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP36 | ENST00000276211.10 | c.133C>A | p.Arg45Ser | missense_variant | 2/12 | 2 | NM_144967.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183456Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67886
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098243Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 1AN XY: 363599
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.133C>A (p.R45S) alteration is located in exon 2 (coding exon 1) of the ARHGAP36 gene. This alteration results from a C to A substitution at nucleotide position 133, causing the arginine (R) at amino acid position 45 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at