chr4-81440901-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_152545.3(RASGEF1B):c.1037A>G(p.Tyr346Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000484 in 1,612,764 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152545.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGEF1B | NM_152545.3 | c.1037A>G | p.Tyr346Cys | missense_variant | 10/14 | ENST00000264400.7 | |
RASGEF1B | NM_001300735.2 | c.1034A>G | p.Tyr345Cys | missense_variant | 10/14 | ||
RASGEF1B | NM_001300736.2 | c.911A>G | p.Tyr304Cys | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGEF1B | ENST00000264400.7 | c.1037A>G | p.Tyr346Cys | missense_variant | 10/14 | 2 | NM_152545.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152218Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000613 AC: 154AN: 251124Hom.: 0 AF XY: 0.000530 AC XY: 72AN XY: 135776
GnomAD4 exome AF: 0.000485 AC: 708AN: 1460428Hom.: 3 Cov.: 28 AF XY: 0.000484 AC XY: 352AN XY: 726564
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152336Hom.: 1 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74494
ClinVar
Submissions by phenotype
RASGEF1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at