chr9-131578589-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001377935.1(RAPGEF1):c.*908C>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 0.274 in 152,358 control chromosomes in the GnomAD database, including 6,746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.27 ( 6733 hom., cov: 33)
Exomes 𝑓: 0.33 ( 13 hom. )
Consequence
RAPGEF1
NM_001377935.1 3_prime_UTR
NM_001377935.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.287
Genes affected
RAPGEF1 (HGNC:4568): (Rap guanine nucleotide exchange factor 1) This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 9-131578589-G-A is Benign according to our data. Variant chr9-131578589-G-A is described in ClinVar as [Benign]. Clinvar id is 1274200.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF1 | NM_001377935.1 | c.*908C>T | 3_prime_UTR_variant | 27/27 | ENST00000683357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF1 | ENST00000683357.1 | c.*908C>T | 3_prime_UTR_variant | 27/27 | NM_001377935.1 |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41705AN: 152036Hom.: 6731 Cov.: 33
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GnomAD4 exome AF: 0.332 AC: 67AN: 202Hom.: 13 Cov.: 0 AF XY: 0.311 AC XY: 46AN XY: 148
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GnomAD4 genome ? AF: 0.274 AC: 41731AN: 152156Hom.: 6733 Cov.: 33 AF XY: 0.275 AC XY: 20427AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 25, 2021 | This variant is associated with the following publications: (PMID: 28171541) - |
Computational scores
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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