rs1305201887
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001003787.4(STRADA):c.947G>A(p.Arg316His) variant causes a missense change. The variant allele was found at a frequency of 0.0000168 in 1,611,906 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. R316C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001003787.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRADA | NM_001003787.4 | c.947G>A | p.Arg316His | missense_variant | 11/13 | ENST00000336174.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRADA | ENST00000336174.12 | c.947G>A | p.Arg316His | missense_variant | 11/13 | 1 | NM_001003787.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248778Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134712
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1459862Hom.: 0 Cov.: 45 AF XY: 0.0000193 AC XY: 14AN XY: 726120
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74266
ClinVar
Submissions by phenotype
Polyhydramnios, megalencephaly, and symptomatic epilepsy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 316 of the STRADA protein (p.Arg316His). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with STRADA-related conditions. ClinVar contains an entry for this variant (Variation ID: 468890). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at