chr5-6662908-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001047.4(SRD5A1):c.655G>A(p.Ala219Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.655G>A | p.Ala219Thr | missense_variant | 4/5 | ENST00000274192.7 | |
SRD5A1 | NM_001324322.2 | c.514G>A | p.Ala172Thr | missense_variant | 3/4 | ||
SRD5A1 | NM_001324323.2 | c.436G>A | p.Ala146Thr | missense_variant | 5/6 | ||
SRD5A1 | NR_136739.2 | n.982G>A | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.655G>A | p.Ala219Thr | missense_variant | 4/5 | 1 | NM_001047.4 | P1 | |
SRD5A1 | ENST00000504286.2 | c.*80G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 2 | ||||
SRD5A1 | ENST00000510531.6 | c.*776G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 2 | ||||
SRD5A1 | ENST00000513117.1 | c.*80G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251452Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135906
GnomAD4 exome AF: 0.000130 AC: 190AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727096
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 2022 | The c.655G>A (p.A219T) alteration is located in exon 4 (coding exon 4) of the SRD5A1 gene. This alteration results from a G to A substitution at nucleotide position 655, causing the alanine (A) at amino acid position 219 to be replaced by a threonine (T). 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