chr3-184302046-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002808.5(PSMD2):c.679G>A(p.Ala227Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002808.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMD2 | NM_002808.5 | c.679G>A | p.Ala227Thr | missense_variant | 5/21 | ENST00000310118.9 | |
PSMD2 | NM_001278708.2 | c.289G>A | p.Ala97Thr | missense_variant | 3/19 | ||
PSMD2 | NM_001278709.2 | c.202G>A | p.Ala68Thr | missense_variant | 3/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMD2 | ENST00000310118.9 | c.679G>A | p.Ala227Thr | missense_variant | 5/21 | 1 | NM_002808.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250698Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135526
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727192
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.0000939 AC XY: 7AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.679G>A (p.A227T) alteration is located in exon 5 (coding exon 5) of the PSMD2 gene. This alteration results from a G to A substitution at nucleotide position 679, causing the alanine (A) at amino acid position 227 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