chr1-94174373-A-G
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004815.4(ARHGAP29):c.3282T>C(p.Thr1094=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,614,132 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0016 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00023 ( 2 hom. )
Consequence
ARHGAP29
NM_004815.4 synonymous
NM_004815.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.323
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 Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-94174373-A-G is Benign according to our data. Variant chr1-94174373-A-G is described in ClinVar as [Benign]. Clinvar id is 791803.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.323 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP29 | NM_004815.4 | c.3282T>C | p.Thr1094= | synonymous_variant | 23/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.3282T>C | p.Thr1094= | synonymous_variant | 23/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000552844.5 | c.3051+231T>C | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00157 AC: 239AN: 152128Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000414 AC: 104AN: 251396Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135868
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GnomAD4 exome AF: 0.000235 AC: 343AN: 1461886Hom.: 2 Cov.: 35 AF XY: 0.000237 AC XY: 172AN XY: 727248
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
ARHGAP29-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 26, 2019 | This variant is classified as 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 | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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