rs1057519061
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000348.4(SRD5A2):c.548-9T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 1,458,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000348.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A2 | NM_000348.4 | c.548-9T>G | intron_variant | Intron 3 of 4 | ENST00000622030.2 | NP_000339.2 | ||
SRD5A2 | XM_011533069.3 | c.326-9T>G | intron_variant | Intron 3 of 4 | XP_011531371.1 | |||
SRD5A2 | XM_011533072.3 | c.293-9T>G | intron_variant | Intron 5 of 6 | XP_011531374.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 246990Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133886
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458602Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 6AN XY: 725036
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency Uncertain:2
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This sequence change falls in intron 3 of the SRD5A2 gene. It does not directly change the encoded amino acid sequence of the SRD5A2 protein. This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has been observed in individual(s) with 5α-RD2 deficiency (PMID: 31186340). ClinVar contains an entry for this variant (Variation ID: 375328). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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