17-38428528-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001199417.2(ARHGAP23):c.43C>T(p.Pro15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,454,718 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001199417.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP23 | ENST00000622683.5 | c.43C>T | p.Pro15Ser | missense_variant | Exon 1 of 24 | 5 | NM_001199417.2 | ENSP00000481862.1 | ||
ARHGAP23 | ENST00000620417.4 | c.43C>T | p.Pro15Ser | missense_variant | Exon 1 of 25 | 5 | ENSP00000482992.1 | |||
ARHGAP23 | ENST00000633445.2 | c.9+9129C>T | intron_variant | Intron 1 of 23 | 3 | ENSP00000516484.1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152092Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000251 AC: 19AN: 75640Hom.: 1 AF XY: 0.000367 AC XY: 16AN XY: 43538
GnomAD4 exome AF: 0.000164 AC: 214AN: 1302518Hom.: 3 Cov.: 30 AF XY: 0.000195 AC XY: 125AN XY: 641846
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.43C>T (p.P15S) alteration is located in exon 1 (coding exon 1) of the ARHGAP23 gene. This alteration results from a C to T substitution at nucleotide position 43, causing the proline (P) at amino acid position 15 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