17-38428541-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001199417.2(ARHGAP23):c.56C>T(p.Pro19Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000358 in 1,451,706 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP23 | ENST00000622683.5 | c.56C>T | p.Pro19Leu | missense_variant | Exon 1 of 24 | 5 | NM_001199417.2 | ENSP00000481862.1 | ||
ARHGAP23 | ENST00000620417.4 | c.56C>T | p.Pro19Leu | missense_variant | Exon 1 of 25 | 5 | ENSP00000482992.1 | |||
ARHGAP23 | ENST00000633445.2 | c.9+9142C>T | intron_variant | Intron 1 of 23 | 3 | ENSP00000516484.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000934 AC: 7AN: 74954Hom.: 0 AF XY: 0.0000926 AC XY: 4AN XY: 43198
GnomAD4 exome AF: 0.0000392 AC: 51AN: 1299612Hom.: 1 Cov.: 30 AF XY: 0.0000469 AC XY: 30AN XY: 640282
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56C>T (p.P19L) 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 56, causing the proline (P) at amino acid position 19 to be replaced by a leucine (L). 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