Variant rs2700 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001042618.2(PARP2):c.*9A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,607,518 control chromosomes in the GnomAD database, including 65,395 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 0.23 ( 4699 hom., cov: 32)

Exomes 𝑓: 0.29 ( 60696 hom. )

Consequence

PARP2
NM_001042618.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.155

Variant links:

Genes affected

PARP2 (HGNC:272): (poly(ADP-ribose) polymerase 2) This gene encodes poly(ADP-ribosyl)transferase-like 2 protein, which contains a catalytic domain and is capable of catalyzing a poly(ADP-ribosyl)ation reaction. This protein has a catalytic domain which is homologous to that of poly (ADP-ribosyl) transferase, but lacks an N-terminal DNA binding domain which activates the C-terminal catalytic domain of poly (ADP-ribosyl) transferase. The basic residues within the N-terminal region of this protein may bear potential DNA-binding properties, and may be involved in the nuclear and/or nucleolar targeting of the protein. Two alternatively spliced transcript variants encoding distinct isoforms have been found. [provided by RefSeq, Jul 2008]

PARP2 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARP2	NM_001042618.2 linkuse as main transcript	c.*9A>C		3_prime_UTR_variant	16/16	ENST00000429687.8	NP_001036083.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARP2	ENST00000429687.8 linkuse as main transcript	c.*9A>C	3_prime_UTR_variant	16/16	1	NM_001042618.2	ENSP00000392972	P2	Q9UGN5-2
PARP2	ENST00000250416.9 linkuse as main transcript	c.*9A>C	3_prime_UTR_variant	16/16	1		ENSP00000250416	A2	Q9UGN5-1
PARP2	ENST00000527915.5 linkuse as main transcript	c.*282A>C	3_prime_UTR_variant	15/15	2		ENSP00000432283
PARP2	ENST00000539930.1 linkuse as main transcript		downstream_gene_variant		3		ENSP00000445524

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35141

AN:

152060

Hom.:

4703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0940

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.280

AC:

68499

AN:

244884

Hom.:

10053

AF XY:

0.285

AC XY:

37825

AN XY:

132806

show subpopulations

Gnomad AFR exome

AF:

0.0897

Gnomad AMR exome

AF:

0.262

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.277

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.307

Gnomad NFE exome

AF:

0.289

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.286

AC:

416019

AN:

1455340

Hom.:

60696

Cov.:

AF XY:

0.288

AC XY:

208675

AN XY:

723900

show subpopulations

Gnomad4 AFR exome

AF:

0.0915

Gnomad4 AMR exome

AF:

0.253

Gnomad4 ASJ exome

AF:

0.253

Gnomad4 EAS exome

AF:

0.271

Gnomad4 SAS exome

AF:

0.344

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.290

Gnomad4 OTH exome

AF:

0.272

GnomAD4 genome

AF:

0.231

AC:

35140

AN:

152178

Hom.:

4699

Cov.:

AF XY:

0.231

AC XY:

17217

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0939

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.261

Gnomad4 EAS

AF:

0.278

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.244

Alfa

AF:

0.266

Hom.:

7419

Bravo

AF:

0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.2

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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