rs372229032
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_001003787.4(STRADA):c.922G>A(p.Glu308Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000166 in 1,597,924 control chromosomes in the GnomAD database, including 1 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001003787.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRADA | ENST00000336174.12 | c.922G>A | p.Glu308Lys | missense_variant | Exon 11 of 13 | 1 | NM_001003787.4 | ENSP00000336655.6 | ||
ENSG00000125695 | ENST00000580553.1 | n.*836G>A | non_coding_transcript_exon_variant | Exon 10 of 12 | 5 | ENSP00000464100.1 | ||||
ENSG00000125695 | ENST00000580553.1 | n.*836G>A | 3_prime_UTR_variant | Exon 10 of 12 | 5 | ENSP00000464100.1 |
Frequencies
GnomAD3 genomes AF: 0.000141 AC: 21AN: 149148Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000124 AC: 30AN: 242468Hom.: 1 AF XY: 0.000153 AC XY: 20AN XY: 130832
GnomAD4 exome AF: 0.000169 AC: 245AN: 1448776Hom.: 1 Cov.: 44 AF XY: 0.000161 AC XY: 116AN XY: 719562
GnomAD4 genome AF: 0.000141 AC: 21AN: 149148Hom.: 0 Cov.: 31 AF XY: 0.000179 AC XY: 13AN XY: 72468
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.922G>A (p.E308K) alteration is located in exon 11 (coding exon 10) of the STRADA gene. This alteration results from a G to A substitution at nucleotide position 922, causing the glutamic acid (E) at amino acid position 308 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Polyhydramnios, megalencephaly, and symptomatic epilepsy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at