11-110580382-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001384657.1(ARHGAP20):c.2564G>T(p.Arg855Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000444 in 1,614,220 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001384657.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP20 | NM_001384657.1 | c.2564G>T | p.Arg855Leu | missense_variant | 15/15 | ENST00000683387.1 | NP_001371586.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP20 | ENST00000683387.1 | c.2564G>T | p.Arg855Leu | missense_variant | 15/15 | NM_001384657.1 | ENSP00000507405 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000446 AC: 112AN: 251248Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135776
GnomAD4 exome AF: 0.000451 AC: 660AN: 1461892Hom.: 1 Cov.: 33 AF XY: 0.000429 AC XY: 312AN XY: 727246
GnomAD4 genome AF: 0.000368 AC: 56AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.2564G>T (p.R855L) alteration is located in exon 16 (coding exon 15) of the ARHGAP20 gene. This alteration results from a G to T substitution at nucleotide position 2564, causing the arginine (R) at amino acid position 855 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