rs11177325
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001010942.3(RAP1B):c.*11949C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,798 control chromosomes in the GnomAD database, including 4,600 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 0.22 ( 4599 hom., cov: 31)
Exomes 𝑓: 0.25 ( 1 hom. )
Consequence
RAP1B
NM_001010942.3 3_prime_UTR
NM_001010942.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.316
Genes affected
RAP1B (HGNC:9857): (RAP1B, member of RAS oncogene family) This gene encodes a member of the RAS-like small GTP-binding protein superfamily. Members of this family regulate multiple cellular processes including cell adhesion and growth and differentiation. This protein localizes to cellular membranes and has been shown to regulate integrin-mediated cell signaling. This protein also plays a role in regulating outside-in signaling in platelets. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 5, 6 and 9. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAP1B | NM_001010942.3 | c.*11949C>T | 3_prime_UTR_variant | 8/8 | ENST00000250559.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAP1B | ENST00000250559.14 | c.*11949C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_001010942.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.225 AC: 34139AN: 151670Hom.: 4605 Cov.: 31
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GnomAD4 exome AF: 0.250 AC: 3AN: 12Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2AN XY: 8
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GnomAD4 genome AF: 0.225 AC: 34132AN: 151786Hom.: 4599 Cov.: 31 AF XY: 0.221 AC XY: 16425AN XY: 74166
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ClinVar
Not reported inComputational scores
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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