14-32091923-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001030055.2(ARHGAP5):āc.1254A>Gā(p.Val418=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 1,613,700 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.016 ( 72 hom., cov: 32)
Exomes š: 0.0018 ( 67 hom. )
Consequence
ARHGAP5
NM_001030055.2 synonymous
NM_001030055.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.648
Genes affected
ARHGAP5 (HGNC:675): (Rho GTPase activating protein 5) Rho GTPase activating protein 5 negatively regulates RHO GTPases, a family which may mediate cytoskeleton changes by stimulating the hydrolysis of bound GTP. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 14-32091923-A-G is Benign according to our data. Variant chr14-32091923-A-G is described in ClinVar as [Benign]. Clinvar id is 786247.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.648 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP5 | NM_001030055.2 | c.1254A>G | p.Val418= | synonymous_variant | 2/7 | ENST00000345122.8 | |
ARHGAP5 | NM_001173.3 | c.1254A>G | p.Val418= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP5 | ENST00000345122.8 | c.1254A>G | p.Val418= | synonymous_variant | 2/7 | 5 | NM_001030055.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2453AN: 152078Hom.: 72 Cov.: 32
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GnomAD3 exomes AF: 0.00444 AC: 1110AN: 249822Hom.: 35 AF XY: 0.00346 AC XY: 469AN XY: 135410
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GnomAD4 exome AF: 0.00177 AC: 2593AN: 1461504Hom.: 67 Cov.: 33 AF XY: 0.00153 AC XY: 1111AN XY: 727048
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GnomAD4 genome AF: 0.0162 AC: 2468AN: 152196Hom.: 72 Cov.: 32 AF XY: 0.0155 AC XY: 1154AN XY: 74422
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at