X-131084258-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_144967.4(ARHGAP36):c.599C>T(p.Ala200Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000505 in 1,208,734 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A200D) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP36 | NM_144967.4 | c.599C>T | p.Ala200Val | missense_variant | 5/12 | ENST00000276211.10 | |
ARHGAP36 | NM_001282607.2 | c.563C>T | p.Ala188Val | missense_variant | 5/12 | ||
ARHGAP36 | NM_001330651.1 | c.191C>T | p.Ala64Val | missense_variant | 4/11 | ||
ARHGAP36 | XM_011531280.2 | c.191C>T | p.Ala64Val | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP36 | ENST00000276211.10 | c.599C>T | p.Ala200Val | missense_variant | 5/12 | 2 | NM_144967.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112356Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34526
GnomAD3 exomes AF: 0.0000335 AC: 6AN: 179224Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63888
GnomAD4 exome AF: 0.0000538 AC: 59AN: 1096378Hom.: 0 Cov.: 31 AF XY: 0.0000470 AC XY: 17AN XY: 361926
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112356Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34526
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.599C>T (p.A200V) alteration is located in exon 5 (coding exon 4) of the ARHGAP36 gene. This alteration results from a C to T substitution at nucleotide position 599, causing the alanine (A) at amino acid position 200 to be replaced by a valine (V). 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