Variant chr6-31623121-C-T 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.112+220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 758,090 control chromosomes in the GnomAD database, including 61,698 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 0.30 ( 8633 hom., cov: 32)

Exomes 𝑓: 0.40 ( 53065 hom. )

Consequence

PRRC2A
NM_004638.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.172

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:

SNORA38 (HGNC:):

SNORA38 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
PRRC2A	NM_004638.4 linkuse as main transcript	c.112+220C>T	intron_variant		ENST00000376033.3	NP_004629.3	P48634-1A0A1U9X974
PRRC2A	NM_080686.3 linkuse as main transcript	c.112+220C>T	intron_variant			NP_542417.2	P48634-1A0A1U9X974
PRRC2A	XM_047419336.1 linkuse as main transcript	c.112+220C>T	intron_variant			XP_047275292.1
SNORA38	NR_002971.1 linkuse as main transcript	n.43C>T	non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PRRC2A	ENST00000376033.3 linkuse as main transcript	c.112+220C>T	intron_variant		1	NM_004638.4	ENSP00000365201.2	P48634-1
PRRC2A	ENST00000376007.8 linkuse as main transcript	c.112+220C>T	intron_variant		1		ENSP00000365175.4	P48634-1
SNORA38	ENST00000363946.1 linkuse as main transcript	n.43C>T	non_coding_transcript_exon_variant	1/1	6
PRRC2A	ENST00000469577.5 linkuse as main transcript	n.136-1140C>T	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45634

AN:

151836

Hom.:

8625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0798

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.590

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.330

GnomAD3 exomes

AF:

0.408

AC:

95559

AN:

233992

Hom.:

21441

AF XY:

0.419

AC XY:

53904

AN XY:

128694

show subpopulations

Gnomad AFR exome

AF:

0.0713

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.560

Gnomad EAS exome

AF:

0.582

Gnomad SAS exome

AF:

0.528

Gnomad FIN exome

AF:

0.322

Gnomad NFE exome

AF:

0.385

Gnomad OTH exome

AF:

0.399

GnomAD4 exome

AF:

0.405

AC:

245316

AN:

606136

Hom.:

53065

Cov.:

AF XY:

0.417

AC XY:

138179

AN XY:

331616

show subpopulations

Gnomad4 AFR exome

AF:

0.0824

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.570

Gnomad4 SAS exome

AF:

0.524

Gnomad4 FIN exome

AF:

0.317

Gnomad4 NFE exome

AF:

0.382

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.300

AC:

45653

AN:

151954

Hom.:

8633

Cov.:

AF XY:

0.306

AC XY:

22695

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.0798

Gnomad4 AMR

AF:

0.348

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.590

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.366

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.368

Hom.:

7310

Bravo

AF:

0.290

Asia WGS

AF:

0.540

AC:

1877

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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