chr4-147906644-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_024605.4(ARHGAP10):c.1041C>T(p.Gly347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 1,613,932 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0072 ( 56 hom. )
Consequence
ARHGAP10
NM_024605.4 synonymous
NM_024605.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.07
Genes affected
ARHGAP10 (HGNC:26099): (Rho GTPase activating protein 10) Predicted to enable GTPase activator activity. Predicted to be involved in cytoskeleton organization and negative regulation of apoptotic process. Predicted to be located in perinuclear region of cytoplasm and plasma membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 4-147906644-C-T is Benign according to our data. Variant chr4-147906644-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2655117.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.07 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP10 | NM_024605.4 | c.1041C>T | p.Gly347= | synonymous_variant | 11/23 | ENST00000336498.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP10 | ENST00000336498.8 | c.1041C>T | p.Gly347= | synonymous_variant | 11/23 | 1 | NM_024605.4 | P1 | |
ARHGAP10 | ENST00000506054.5 | n.6173C>T | non_coding_transcript_exon_variant | 5/17 | 1 | ||||
ARHGAP10 | ENST00000507661.1 | c.75C>T | p.Gly25= | synonymous_variant | 2/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00466 AC: 709AN: 152042Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00458 AC: 1152AN: 251418Hom.: 6 AF XY: 0.00470 AC XY: 638AN XY: 135882
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GnomAD4 exome AF: 0.00716 AC: 10471AN: 1461772Hom.: 56 Cov.: 33 AF XY: 0.00689 AC XY: 5011AN XY: 727182
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GnomAD4 genome ? AF: 0.00466 AC: 709AN: 152160Hom.: 3 Cov.: 33 AF XY: 0.00472 AC XY: 351AN XY: 74382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | ARHGAP10: BP4, BP7, BS2 - |
Computational scores
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Name
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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