2-33457670-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000402538.7(RASGRP3):c.-261+9727G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,704 control chromosomes in the GnomAD database, including 32,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (★).
Frequency
Genomes: 𝑓 0.66 ( 32872 hom., cov: 29)
Consequence
RASGRP3
ENST00000402538.7 intron
ENST00000402538.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.150
Genes affected
RASGRP3 (HGNC:14545): (RAS guanyl releasing protein 3) The protein encoded by this gene is a guanine nucleotide exchange factor that activates the oncogenes HRAS and RAP1A. Defects in this gene have been associated with systemic lupus erythematosus and several cancers. [provided by RefSeq, Mar 2017]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGRP3 | NM_001349975.2 | c.-383+9727G>T | intron_variant | ||||
RASGRP3 | NM_001349978.2 | c.-261+9727G>T | intron_variant | ||||
RASGRP3 | NM_170672.3 | c.-261+9727G>T | intron_variant | ||||
RASGRP3 | XM_011532746.4 | c.-159+9727G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGRP3 | ENST00000402538.7 | c.-261+9727G>T | intron_variant | 1 | P5 | ||||
RASGRP3 | ENST00000479528.5 | n.149+9727G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
RASGRP3 | ENST00000484909.5 | n.390+9727G>T | intron_variant, non_coding_transcript_variant | 2 | |||||
RASGRP3 | ENST00000497723.6 | n.303+9727G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.656 AC: 99418AN: 151586Hom.: 32872 Cov.: 29
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.656 AC: 99458AN: 151704Hom.: 32872 Cov.: 29 AF XY: 0.656 AC XY: 48599AN XY: 74114
GnomAD4 genome
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lip and oral cavity carcinoma Other:1
association, criteria provided, single submitter | case-control | Department of Biological Science, Sunandan Divatia School of Science, NMIMS University | Nov 02, 2015 | The frequency of the homozygous SNP genotypes were observed more in the oral cancer patients in comparison to controls, implying the role of this genotype in predisposition of oral cancer. - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at