chr5-6633581-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001047.4(SRD5A1):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000366 in 1,365,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001047.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.5C>T | p.Ala2Val | missense_variant | 1/5 | ENST00000274192.7 | |
SRD5A1 | NM_001324322.2 | c.31C>T | p.Gln11Ter | stop_gained | 1/4 | ||
SRD5A1 | NM_001324323.2 | c.-717C>T | 5_prime_UTR_variant | 1/6 | |||
SRD5A1 | NR_136739.2 | n.142C>T | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.5C>T | p.Ala2Val | missense_variant | 1/5 | 1 | NM_001047.4 | P1 | |
SRD5A1 | ENST00000504286.2 | c.5C>T | p.Ala2Val | missense_variant, NMD_transcript_variant | 1/6 | 2 | |||
SRD5A1 | ENST00000513117.1 | c.5C>T | p.Ala2Val | missense_variant, NMD_transcript_variant | 1/4 | 2 | |||
SRD5A1 | ENST00000510531.6 | c.5C>T | p.Ala2Val | missense_variant, NMD_transcript_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000176 AC: 2AN: 113554Hom.: 0 AF XY: 0.0000318 AC XY: 2AN XY: 62848
GnomAD4 exome AF: 0.00000366 AC: 5AN: 1365268Hom.: 0 Cov.: 30 AF XY: 0.00000743 AC XY: 5AN XY: 673120
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the SRD5A1 gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a valine (V). 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