rs3130626
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004638.4(PRRC2A):āc.2376A>Gā(p.Val792=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,612,116 control chromosomes in the GnomAD database, including 26,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.17 ( 2375 hom., cov: 32)
Exomes š: 0.18 ( 24306 hom. )
Consequence
PRRC2A
NM_004638.4 synonymous
NM_004638.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0710
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=-0.5).
BP6
?
Variant 6-31630712-A-G is Benign according to our data. Variant chr6-31630712-A-G is described in ClinVar as [Benign]. Clinvar id is 3059728.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.071 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.2376A>G | p.Val792= | synonymous_variant | 15/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.2376A>G | p.Val792= | synonymous_variant | 15/31 | ||
PRRC2A | XM_047419336.1 | c.2376A>G | p.Val792= | synonymous_variant | 15/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.2376A>G | p.Val792= | synonymous_variant | 15/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.2376A>G | p.Val792= | synonymous_variant | 15/31 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.170 AC: 25655AN: 151062Hom.: 2375 Cov.: 32
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GnomAD3 exomes AF: 0.145 AC: 36450AN: 251268Hom.: 2989 AF XY: 0.145 AC XY: 19696AN XY: 135816
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GnomAD4 exome AF: 0.176 AC: 257607AN: 1460932Hom.: 24306 Cov.: 35 AF XY: 0.174 AC XY: 126406AN XY: 726850
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GnomAD4 genome ? AF: 0.170 AC: 25655AN: 151184Hom.: 2375 Cov.: 32 AF XY: 0.165 AC XY: 12207AN XY: 73916
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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 21, 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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BayesDel_noAF
Benign
CADD
Benign
DANN
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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