rs1048854
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004815.4(ARHGAP29):c.2673A>G(p.Gln891=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,613,954 control chromosomes in the GnomAD database, including 51,897 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3793 hom., cov: 32)
Exomes 𝑓: 0.25 ( 48104 hom. )
Consequence
ARHGAP29
NM_004815.4 synonymous
NM_004815.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.397
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
?
Synonymous conserved (PhyloP=0.397 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP29 | NM_004815.4 | c.2673A>G | p.Gln891= | synonymous_variant | 21/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.2673A>G | p.Gln891= | synonymous_variant | 21/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000482481.1 | n.7249A>G | non_coding_transcript_exon_variant | 9/10 | 1 | ||||
ARHGAP29 | ENST00000552844.5 | c.2673A>G | p.Gln891= | synonymous_variant, NMD_transcript_variant | 21/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.197 AC: 29960AN: 152030Hom.: 3795 Cov.: 32
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GnomAD3 exomes AF: 0.219 AC: 55103AN: 251332Hom.: 7008 AF XY: 0.225 AC XY: 30580AN XY: 135840
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GnomAD4 exome AF: 0.249 AC: 364483AN: 1461806Hom.: 48104 Cov.: 35 AF XY: 0.249 AC XY: 181424AN XY: 727206
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GnomAD4 genome ? AF: 0.197 AC: 29958AN: 152148Hom.: 3793 Cov.: 32 AF XY: 0.193 AC XY: 14387AN XY: 74372
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at