chr1-94177673-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004815.4(ARHGAP29):c.2844A>C(p.Thr948=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,613,702 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00074 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
ARHGAP29
NM_004815.4 synonymous
NM_004815.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.421
Genes affected
ARHGAP29 (HGNC:30207): (Rho GTPase activating protein 29) Rap1 is a small GTPase that, through effectors, regulates Rho GTPase signaling. These effectors- Rasip1, Radil, and the protein encoded by this gene- translocate to the cell membrane, where they form a multiprotein complex. This complex is necessary for Rap1-induced inhibition of Rho signaling. Defects in this gene may be a cause of nonsyndromic cleft lip with or without cleft palate. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 1-94177673-T-G is Benign according to our data. Variant chr1-94177673-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3045862.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-94177673-T-G is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP29 | NM_004815.4 | c.2844A>C | p.Thr948= | synonymous_variant | 22/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.2844A>C | p.Thr948= | synonymous_variant | 22/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000482481.1 | n.7420A>C | non_coding_transcript_exon_variant | 10/10 | 1 | ||||
ARHGAP29 | ENST00000552844.5 | c.2844A>C | p.Thr948= | synonymous_variant, NMD_transcript_variant | 22/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000749 AC: 114AN: 152140Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000793 AC: 199AN: 250966Hom.: 1 AF XY: 0.000789 AC XY: 107AN XY: 135648
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GnomAD4 exome AF: 0.00105 AC: 1540AN: 1461444Hom.: 2 Cov.: 31 AF XY: 0.00104 AC XY: 753AN XY: 726982
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ARHGAP29-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 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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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