chr11-128969381-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001378024.1(ARHGAP32):c.5832C>T(p.Ser1944=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,614,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 0 hom. )
Consequence
ARHGAP32
NM_001378024.1 synonymous
NM_001378024.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 11-128969381-G-A is Benign according to our data. Variant chr11-128969381-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041632.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.21 with no splicing effect.
BS2
High AC in GnomAd4 at 212 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP32 | NM_001378024.1 | c.5832C>T | p.Ser1944= | synonymous_variant | 23/23 | ENST00000682385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP32 | ENST00000682385.1 | c.5832C>T | p.Ser1944= | synonymous_variant | 23/23 | NM_001378024.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00144 AC: 362AN: 251472Hom.: 2 AF XY: 0.00163 AC XY: 221AN XY: 135908
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GnomAD4 exome AF: 0.00233 AC: 3406AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00232 AC XY: 1685AN XY: 727248
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GnomAD4 genome AF: 0.00139 AC: 212AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ARHGAP32-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at