4-81448265-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152545.3(RASGEF1B):c.458T>A(p.Val153Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,612,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V153F) has been classified as Uncertain significance.
Frequency
Consequence
NM_152545.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGEF1B | NM_152545.3 | c.458T>A | p.Val153Asp | missense_variant | 5/14 | ENST00000264400.7 | |
RASGEF1B | NM_001300735.2 | c.455T>A | p.Val152Asp | missense_variant | 5/14 | ||
RASGEF1B | NM_001300736.2 | c.332T>A | p.Val111Asp | missense_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGEF1B | ENST00000264400.7 | c.458T>A | p.Val153Asp | missense_variant | 5/14 | 2 | NM_152545.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251282Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135816
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460408Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726534
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.458T>A (p.V153D) alteration is located in exon 5 (coding exon 4) of the RASGEF1B gene. This alteration results from a T to A substitution at nucleotide position 458, causing the valine (V) at amino acid position 153 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at