3-119295013-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020754.4(ARHGAP31):c.100+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,613,586 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
ARHGAP31
NM_020754.4 intron
NM_020754.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0360
Genes affected
ARHGAP31 (HGNC:29216): (Rho GTPase activating protein 31) This gene encodes a GTPase-activating protein (GAP). A variety of cellular processes are regulated by Rho GTPases which cycle between an inactive form bound to GDP and an active form bound to GTP. This cycling between inactive and active forms is regulated by guanine nucleotide exchange factors and GAPs. The encoded protein is a GAP shown to regulate two GTPases involved in protein trafficking and cell growth. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 3-119295013-C-T is Benign according to our data. Variant chr3-119295013-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 342626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 187 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP31 | NM_020754.4 | c.100+9C>T | intron_variant | ENST00000264245.9 | |||
ARHGAP31 | XM_006713714.4 | c.100+9C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP31 | ENST00000264245.9 | c.100+9C>T | intron_variant | 1 | NM_020754.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00123 AC: 187AN: 152084Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000321 AC: 80AN: 249528Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135388
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GnomAD4 exome AF: 0.000109 AC: 160AN: 1461384Hom.: 0 Cov.: 32 AF XY: 0.000103 AC XY: 75AN XY: 727026
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
ARHGAP31-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 05, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2023 | - - |
Computational 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