Variant chr6-31633043-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004638.4(PRRC2A):c.4319+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,450,738 control chromosomes in the GnomAD database, including 24,793 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: 𝑓 0.17 ( 2379 hom., cov: 32)

Exomes 𝑓: 0.18 ( 22414 hom. )

Consequence

PRRC2A
NM_004638.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.10

Variant links:

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]

PRRC2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PRRC2A	NM_004638.4 linkuse as main transcript	c.4319+51A>G	intron_variant	ENST00000376033.3
PRRC2A	NM_080686.3 linkuse as main transcript	c.4319+51A>G	intron_variant
PRRC2A	XM_047419336.1 linkuse as main transcript	c.4319+51A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRRC2A	ENST00000376033.3 linkuse as main transcript	c.4319+51A>G		intron_variant		1	NM_004638.4	P1	P48634-1
PRRC2A	ENST00000376007.8 linkuse as main transcript	c.4319+51A>G		intron_variant		1		P1	P48634-1

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25664

AN:

151982

Hom.:

2379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.0987

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.0788

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.146

AC:

11244

AN:

76768

Hom.:

934

AF XY:

0.149

AC XY:

5898

AN XY:

39502

show subpopulations

Gnomad AFR exome

AF:

0.205

Gnomad AMR exome

AF:

0.0857

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.0965

Gnomad SAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.170

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.147

GnomAD4 exome

AF:

0.180

AC:

234154

AN:

1298638

Hom.:

22414

Cov.:

AF XY:

0.178

AC XY:

112494

AN XY:

631260

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.0879

Gnomad4 ASJ exome

AF:

0.122

Gnomad4 EAS exome

AF:

0.0409

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.169

AC:

25664

AN:

152100

Hom.:

2379

Cov.:

AF XY:

0.164

AC XY:

12218

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.0983

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.0794

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.184

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.178

Hom.:

1670

Bravo

AF:

0.166

Asia WGS

AF:

0.0950

AC:

331

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.27

DANN

Benign

0.32

RBP_binding_hub_radar

0.85

RBP_regulation_power_radar

2.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over