rs767564684
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000348.4(SRD5A2):c.620C>T(p.Ala207Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000348.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A2 | NM_000348.4 | c.620C>T | p.Ala207Val | missense_variant | Exon 4 of 5 | ENST00000622030.2 | NP_000339.2 | |
SRD5A2 | XM_011533069.3 | c.398C>T | p.Ala133Val | missense_variant | Exon 4 of 5 | XP_011531371.1 | ||
SRD5A2 | XM_011533072.3 | c.365C>T | p.Ala122Val | missense_variant | Exon 6 of 7 | XP_011531374.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency Uncertain:1
The observed missense variant c.620C>T(p.Thr207Ile) in SRD5A2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.620C>T(p.Thr207Ile) variant is reported with 0.0004% allele frequency in gnomAD Exomes. It has been submitted to ClinVar as Pathogenic/Likely Pathogenic. However, no details are available for independent assessment. The variant is predicted to be damaging by SIFT. The amino acid Thr at position 207 is changed to a Ile changing protein sequence and it might alter its composition and physico-chemical properties. The reference amino acid p.Thr207Ile in SRD5A2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.