rs3130071
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004638.4(PRRC2A):c.1062T>A(p.Gly354=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 1,608,150 control chromosomes in the GnomAD database, including 627,241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.91 ( 63830 hom., cov: 30)
Exomes 𝑓: 0.88 ( 563411 hom. )
Consequence
PRRC2A
NM_004638.4 synonymous
NM_004638.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.02
Genes affected
PRRC2A (HGNC:13918): (proline rich coiled-coil 2A) A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for TNF alpha and TNF beta. These genes are all within the human major histocompatibility complex class III region. This gene has microsatellite repeats which are associated with the age-at-onset of insulin-dependent diabetes mellitus (IDDM) and possibly thought to be involved with the inflammatory process of pancreatic beta-cell destruction during the development of IDDM. This gene is also a candidate gene for the development of rheumatoid arthritis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 6-31626851-T-A is Benign according to our data. Variant chr6-31626851-T-A is described in ClinVar as [Benign]. Clinvar id is 3060526.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.02 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.1062T>A | p.Gly354= | synonymous_variant | 10/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.1062T>A | p.Gly354= | synonymous_variant | 10/31 | ||
PRRC2A | XM_047419336.1 | c.1062T>A | p.Gly354= | synonymous_variant | 10/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.1062T>A | p.Gly354= | synonymous_variant | 10/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.1062T>A | p.Gly354= | synonymous_variant | 10/31 | 1 | P1 | ||
PRRC2A | ENST00000464890.1 | n.489T>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
PRRC2A | ENST00000469577.5 | n.907T>A | non_coding_transcript_exon_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.914 AC: 139031AN: 152076Hom.: 63766 Cov.: 30
GnomAD3 genomes
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GnomAD3 exomes AF: 0.916 AC: 218713AN: 238852Hom.: 100549 AF XY: 0.916 AC XY: 118966AN XY: 129872
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GnomAD4 exome AF: 0.878 AC: 1278678AN: 1455956Hom.: 563411 Cov.: 61 AF XY: 0.881 AC XY: 637953AN XY: 723796
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GnomAD4 genome ? AF: 0.914 AC: 139153AN: 152194Hom.: 63830 Cov.: 30 AF XY: 0.916 AC XY: 68150AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PRRC2A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at