20-62138230-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002792.4(PSMA7):c.532G>T(p.Asp178Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002792.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMA7 | NM_002792.4 | c.532G>T | p.Asp178Tyr | missense_variant | Exon 5 of 7 | ENST00000370873.9 | NP_002783.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251274Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135814
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461790Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727198
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.532G>T (p.D178Y) alteration is located in exon 5 (coding exon 5) of the PSMA7 gene. This alteration results from a G to T substitution at nucleotide position 532, causing the aspartic acid (D) at amino acid position 178 to be replaced by a tyrosine (Y). 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