chr4-81434650-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_152545.3(RASGEF1B):c.1189G>A(p.Val397Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0132 in 1,590,554 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_152545.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGEF1B | NM_152545.3 | c.1189G>A | p.Val397Ile | missense_variant | 11/14 | ENST00000264400.7 | |
RASGEF1B | NM_001300735.2 | c.1186G>A | p.Val396Ile | missense_variant | 11/14 | ||
RASGEF1B | NM_001300736.2 | c.1063G>A | p.Val355Ile | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGEF1B | ENST00000264400.7 | c.1189G>A | p.Val397Ile | missense_variant | 11/14 | 2 | NM_152545.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00970 AC: 1476AN: 152124Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00942 AC: 2367AN: 251142Hom.: 21 AF XY: 0.00936 AC XY: 1271AN XY: 135720
GnomAD4 exome AF: 0.0136 AC: 19499AN: 1438312Hom.: 171 Cov.: 27 AF XY: 0.0131 AC XY: 9382AN XY: 717148
GnomAD4 genome ? AF: 0.00968 AC: 1474AN: 152242Hom.: 13 Cov.: 32 AF XY: 0.00939 AC XY: 699AN XY: 74430
ClinVar
Submissions by phenotype
RASGEF1B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2020 | This variant is classified as 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