Genetic Variant PARP2:c.1102-51G>T (chr14-20356256-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001042618.2(PARP2):c.1102-51G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,597,880 control chromosomes in the GnomAD database, including 49,171 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 0.20 ( 3659 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45512 hom. )

Consequence

PARP2
NM_001042618.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.354

Publications

23 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP2	NM_001042618.2 link	c.1102-51G>T		intron_variant	Intron 11 of 15	ENST00000429687.8	NP_001036083.1	Q9UGN5-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP2	ENST00000429687.8 link	c.1102-51G>T		intron_variant	Intron 11 of 15	1	NM_001042618.2	ENSP00000392972.3		Q9UGN5-2

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

30993

AN:

151920

Hom.:

3660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0904

Gnomad AMI

AF:

0.153

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.272

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.206

GnomAD2 exomes

AF:

0.247

AC:

60379

AN:

244114

AF XY:

0.252

show subpopulations

Gnomad AFR exome

AF:

0.0870

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.199

Gnomad EAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.283

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.248

GnomAD4 exome

AF:

0.247

AC:

356770

AN:

1445844

Hom.:

45512

Cov.:

AF XY:

0.250

AC XY:

179464

AN XY:

718924

show subpopulations

African (AFR)

AF:

0.0870

AC:

2871

AN:

33004

American (AMR)

AF:

0.227

AC:

9860

AN:

43500

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

5005

AN:

25656

East Asian (EAS)

AF:

0.261

AC:

10310

AN:

39542

South Asian (SAS)

AF:

0.327

AC:

27804

AN:

84948

European-Finnish (FIN)

AF:

0.281

AC:

14916

AN:

53140

Middle Eastern (MID)

AF:

0.186

AC:

1061

AN:

5706

European-Non Finnish (NFE)

AF:

0.246

AC:

270879

AN:

1100652

Other (OTH)

AF:

0.236

AC:

14064

AN:

59696

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

12156

24312

36468

48624

60780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.204

AC:

30996

AN:

152036

Hom.:

3659

Cov.:

AF XY:

0.205

AC XY:

15255

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.0902

AC:

3740

AN:

41460

American (AMR)

AF:

0.201

AC:

3074

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

722

AN:

3466

East Asian (EAS)

AF:

0.273

AC:

1404

AN:

5150

South Asian (SAS)

AF:

0.344

AC:

1658

AN:

4824

European-Finnish (FIN)

AF:

0.286

AC:

3016

AN:

10558

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.246

AC:

16752

AN:

67978

Other (OTH)

AF:

0.207

AC:

438

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1228

2456

3684

4912

6140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.232

Hom.:

19607

Bravo

AF:

0.190

Asia WGS

AF:

0.288

AC:

1003

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

4.4

(source)

DANN

Benign

0.41

PhyloP100

0.35

PromoterAI

-0.014

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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14-20356256-G-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over