6-31635993-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004638.4(PRRC2A):āc.5568A>Gā(p.Gln1856=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,611,550 control chromosomes in the GnomAD database, including 26,628 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 ( 2376 hom., cov: 31)
Exomes š: 0.18 ( 24252 hom. )
Consequence
PRRC2A
NM_004638.4 synonymous
NM_004638.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.240
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 6-31635993-A-G is Benign according to our data. Variant chr6-31635993-A-G is described in ClinVar as [Benign]. Clinvar id is 3060509.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.5568A>G | p.Gln1856= | synonymous_variant | 25/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.5568A>G | p.Gln1856= | synonymous_variant | 25/31 | ||
PRRC2A | XM_047419336.1 | c.5568A>G | p.Gln1856= | synonymous_variant | 25/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.5568A>G | p.Gln1856= | synonymous_variant | 25/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.5568A>G | p.Gln1856= | synonymous_variant | 25/31 | 1 | P1 | ||
PRRC2A | ENST00000487089.1 | n.634A>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
PRRC2A | ENST00000487839.1 | n.502A>G | non_coding_transcript_exon_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25658AN: 151856Hom.: 2376 Cov.: 31
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GnomAD3 exomes AF: 0.145 AC: 36390AN: 251022Hom.: 2991 AF XY: 0.145 AC XY: 19657AN XY: 135668
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GnomAD4 exome AF: 0.176 AC: 256703AN: 1459576Hom.: 24252 Cov.: 35 AF XY: 0.174 AC XY: 126020AN XY: 726238
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GnomAD4 genome AF: 0.169 AC: 25658AN: 151974Hom.: 2376 Cov.: 31 AF XY: 0.164 AC XY: 12202AN XY: 74264
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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
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RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at