11-128965863-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378024.1(ARHGAP32):c.*3044G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,228 control chromosomes in the GnomAD database, including 59,743 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.88 ( 59742 hom., cov: 31)
Exomes 𝑓: 1.0 ( 1 hom. )
Consequence
ARHGAP32
NM_001378024.1 3_prime_UTR
NM_001378024.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.381
Genes affected
ARHGAP32 (HGNC:17399): (Rho GTPase activating protein 32) RICS is a neuron-associated GTPase-activating protein that may regulate dendritic spine morphology and strength by modulating Rho GTPase (see RHOA; MIM 165390) activity (Okabe et al., 2003 [PubMed 12531901]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP32 | NM_001378024.1 | c.*3044G>A | 3_prime_UTR_variant | 23/23 | ENST00000682385.1 | NP_001364953.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP32 | ENST00000682385.1 | c.*3044G>A | 3_prime_UTR_variant | 23/23 | NM_001378024.1 | ENSP00000507720 | P3 | |||
ARHGAP32 | ENST00000310343.13 | c.*3044G>A | 3_prime_UTR_variant | 22/22 | 1 | ENSP00000310561 | A1 |
Frequencies
GnomAD3 genomes AF: 0.885 AC: 134556AN: 152108Hom.: 59703 Cov.: 31
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GnomAD4 exome AF: 1.00 AC: 2AN: 2Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2AN XY: 2
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GnomAD4 genome AF: 0.885 AC: 134650AN: 152226Hom.: 59742 Cov.: 31 AF XY: 0.882 AC XY: 65606AN XY: 74420
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at