1-161048400-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001025598.2(ARHGAP30):c.2621G>A(p.Cys874Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001025598.2 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 |
---|---|---|---|---|---|---|---|
ARHGAP30 | NM_001025598.2 | c.2621G>A | p.Cys874Tyr | missense_variant | 12/12 | ENST00000368013.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP30 | ENST00000368013.8 | c.2621G>A | p.Cys874Tyr | missense_variant | 12/12 | 2 | NM_001025598.2 | P2 | |
ARHGAP30 | ENST00000368015.1 | c.2090G>A | p.Cys697Tyr | missense_variant | 8/8 | 5 | |||
ARHGAP30 | ENST00000368016.7 | c.2033-45G>A | intron_variant | 5 | A2 | ||||
ARHGAP30 | ENST00000461003.5 | n.3403G>A | non_coding_transcript_exon_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251314Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135816
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461830Hom.: 0 Cov.: 43 AF XY: 0.0000261 AC XY: 19AN XY: 727220
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.2621G>A (p.C874Y) alteration is located in exon 12 (coding exon 12) of the ARHGAP30 gene. This alteration results from a G to A substitution at nucleotide position 2621, causing the cysteine (C) at amino acid position 874 to be replaced by a tyrosine (Y). 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