17-81868514-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001301242.2(ARHGDIA):c.865G>T(p.Gly289Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000525 in 1,530,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001301242.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGDIA | NM_004309.6 | c.*362G>T | 3_prime_UTR_variant | 6/6 | ENST00000269321.12 | NP_004300.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGDIA | ENST00000269321 | c.*362G>T | 3_prime_UTR_variant | 6/6 | 1 | NM_004309.6 | ENSP00000269321.7 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000336 AC: 44AN: 130958Hom.: 0 AF XY: 0.000364 AC XY: 26AN XY: 71412
GnomAD4 exome AF: 0.000545 AC: 751AN: 1378328Hom.: 0 Cov.: 32 AF XY: 0.000527 AC XY: 358AN XY: 679322
GnomAD4 genome AF: 0.000342 AC: 52AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74354
ClinVar
Submissions by phenotype
Nephrotic syndrome, type 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Dr.Nikuei Genetic Center | Jun 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at