chr20-62139808-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002792.4(PSMA7):c.321C>T(p.Ile107=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000142 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
PSMA7
NM_002792.4 synonymous
NM_002792.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.51
Genes affected
PSMA7 (HGNC:9536): (proteasome 20S subunit alpha 7) 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. 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 peptidase T1A family that functions as a 20S core alpha subunit. The encoded protein interacts with the hepatitis B virus X protein and plays a role in regulating hepatitis C virus internal ribosome entry site (IRES) activity, an activity essential for viral replication. The encoded protein also plays a role in the cellular stress response by regulating hypoxia-inducible factor-1alpha. A pseudogene of this gene is located on the long arm of chromosome 9. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 20-62139808-G-A is Benign according to our data. Variant chr20-62139808-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 754641.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMA7 | NM_002792.4 | c.321C>T | p.Ile107= | synonymous_variant | 3/7 | ENST00000370873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMA7 | ENST00000370873.9 | c.321C>T | p.Ile107= | synonymous_variant | 3/7 | 1 | NM_002792.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152266Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000346 AC: 87AN: 251110Hom.: 1 AF XY: 0.000287 AC XY: 39AN XY: 135844
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GnomAD4 exome AF: 0.000143 AC: 209AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 98AN XY: 727172
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GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74398
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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