chr20-38497421-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_020336.4(RALGAPB):c.458G>A(p.Arg153His) variant causes a missense change. The variant allele was found at a frequency of 0.0000266 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R153C) has been classified as Uncertain significance.
Frequency
Consequence
NM_020336.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RALGAPB | NM_020336.4 | c.458G>A | p.Arg153His | missense_variant | 4/30 | ENST00000262879.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RALGAPB | ENST00000262879.11 | c.458G>A | p.Arg153His | missense_variant | 4/30 | 1 | NM_020336.4 | P4 | |
RALGAPB | ENST00000397040.5 | c.458G>A | p.Arg153His | missense_variant | 4/30 | 1 | P4 | ||
RALGAPB | ENST00000397042.7 | c.458G>A | p.Arg153His | missense_variant | 4/30 | 1 | A1 | ||
RALGAPB | ENST00000495949.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251398Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135862
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727136
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152142Hom.: 0 Cov.: 31 AF XY: 0.0000942 AC XY: 7AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.458G>A (p.R153H) alteration is located in exon 4 (coding exon 3) of the RALGAPB gene. This alteration results from a G to A substitution at nucleotide position 458, causing the arginine (R) at amino acid position 153 to be replaced by a histidine (H). 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