rs9916279
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002809.4(PSMD3):āc.849T>Cā(p.Asn283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,613,698 control chromosomes in the GnomAD database, including 23,892 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.20 ( 3880 hom., cov: 32)
Exomes š: 0.16 ( 20012 hom. )
Consequence
PSMD3
NM_002809.4 synonymous
NM_002809.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.13
Genes affected
PSMD3 (HGNC:9560): (proteasome 26S subunit, non-ATPase 3) The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. This gene encodes a member of the proteasome subunit S3 family that functions as one of the non-ATPase subunits of the 19S regulator lid. Single nucleotide polymorphisms in this gene are associated with neutrophil count. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP7
?
Synonymous conserved (PhyloP=-1.13 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMD3 | NM_002809.4 | c.849T>C | p.Asn283= | synonymous_variant | 5/12 | ENST00000264639.9 | |
LOC124904000 | XR_007065751.1 | n.3356-1006A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMD3 | ENST00000264639.9 | c.849T>C | p.Asn283= | synonymous_variant | 5/12 | 1 | NM_002809.4 | P1 | |
PSMD3 | ENST00000540504.2 | c.296+108T>C | intron_variant | 3 | |||||
PSMD3 | ENST00000580980.1 | n.329T>C | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
PSMD3 | ENST00000415039.7 | c.*323T>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30628AN: 152008Hom.: 3880 Cov.: 32
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GnomAD3 exomes AF: 0.140 AC: 35112AN: 251178Hom.: 3197 AF XY: 0.135 AC XY: 18288AN XY: 135756
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GnomAD4 exome AF: 0.156 AC: 228571AN: 1461572Hom.: 20012 Cov.: 33 AF XY: 0.153 AC XY: 111575AN XY: 727036
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GnomAD4 genome ? AF: 0.201 AC: 30648AN: 152126Hom.: 3880 Cov.: 32 AF XY: 0.197 AC XY: 14632AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at