5-6633595-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001047.4(SRD5A1):c.19G>A(p.Val7Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000046 in 1,520,820 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 (★).
Frequency
Consequence
NM_001047.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.19G>A | p.Val7Met | missense_variant | 1/5 | ENST00000274192.7 | |
SRD5A1 | NM_001324322.2 | c.45G>A | p.Gly15= | synonymous_variant | 1/4 | ||
SRD5A1 | NM_001324323.2 | c.-703G>A | 5_prime_UTR_variant | 1/6 | |||
SRD5A1 | NR_136739.2 | n.156G>A | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.19G>A | p.Val7Met | missense_variant | 1/5 | 1 | NM_001047.4 | P1 | |
SRD5A1 | ENST00000504286.2 | c.19G>A | p.Val7Met | missense_variant, NMD_transcript_variant | 1/6 | 2 | |||
SRD5A1 | ENST00000513117.1 | c.19G>A | p.Val7Met | missense_variant, NMD_transcript_variant | 1/4 | 2 | |||
SRD5A1 | ENST00000510531.6 | c.19G>A | p.Val7Met | missense_variant, NMD_transcript_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000259 AC: 3AN: 115748Hom.: 0 AF XY: 0.0000156 AC XY: 1AN XY: 64088
GnomAD4 exome AF: 0.00000292 AC: 4AN: 1368630Hom.: 0 Cov.: 30 AF XY: 0.00000296 AC XY: 2AN XY: 675084
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.19G>A (p.V7M) alteration is located in exon 1 (coding exon 1) of the SRD5A1 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the valine (V) at amino acid position 7 to be replaced by a methionine (M). 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