dbSNP rs2269996: PARP12:n.*703C>T (chr7-140024558-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000473341.5(PARP12):n.*703C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,613,240 control chromosomes in the GnomAD database, including 42,837 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 0.26 ( 5724 hom., cov: 32)

Exomes 𝑓: 0.21 ( 37113 hom. )

Consequence

PARP12
ENST00000473341.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

17 publications found

Variant links:

Genes affected

PARP12 (HGNC:21919): (poly(ADP-ribose) polymerase family member 12) Enables protein ADP-ribosylase activity. Involved in protein auto-ADP-ribosylation and protein mono-ADP-ribosylation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PARP12 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.021).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PARP12	NM_022750.4 link	c.*2C>T	3_prime_UTR_variant	Exon 12 of 12	ENST00000263549.8	NP_073587.1	Q9H0J9A4D1T0
PARP12	NR_130117.2 link	n.2070C>T	non_coding_transcript_exon_variant	Exon 11 of 11
PARP12	XM_047420739.1 link	c.*2C>T	3_prime_UTR_variant	Exon 12 of 12		XP_047276695.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP12	ENST00000263549.8 link	c.*2C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_022750.4	ENSP00000263549.3		Q9H0J9

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39020

AN:

151966

Hom.:

5710

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.269

GnomAD2 exomes

AF:

0.263

AC:

65991

AN:

250768

AF XY:

0.249

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.435

Gnomad ASJ exome

AF:

0.187

Gnomad EAS exome

AF:

0.584

Gnomad FIN exome

AF:

0.171

Gnomad NFE exome

AF:

0.206

Gnomad OTH exome

AF:

0.234

GnomAD4 exome

AF:

0.210

AC:

306889

AN:

1461156

Hom.:

37113

Cov.:

AF XY:

0.207

AC XY:

150682

AN XY:

726902

show subpopulations

African (AFR)

AF:

0.316

AC:

10567

AN:

33468

American (AMR)

AF:

0.425

AC:

18964

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

4920

AN:

26124

East Asian (EAS)

AF:

0.573

AC:

22738

AN:

39692

South Asian (SAS)

AF:

0.153

AC:

13195

AN:

86224

European-Finnish (FIN)

AF:

0.174

AC:

9264

AN:

53384

Middle Eastern (MID)

AF:

0.157

AC:

906

AN:

5768

European-Non Finnish (NFE)

AF:

0.192

AC:

213025

AN:

1111450

Other (OTH)

AF:

0.220

AC:

13310

AN:

60376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

12658

25316

37973

50631

63289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7566

15132

22698

30264

37830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.257

AC:

39056

AN:

152084

Hom.:

5724

Cov.:

AF XY:

0.257

AC XY:

19086

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.311

AC:

12905

AN:

41448

American (AMR)

AF:

0.366

AC:

5601

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

633

AN:

3472

East Asian (EAS)

AF:

0.560

AC:

2891

AN:

5158

South Asian (SAS)

AF:

0.158

AC:

761

AN:

4820

European-Finnish (FIN)

AF:

0.164

AC:

1735

AN:

10588

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13733

AN:

67986

Other (OTH)

AF:

0.269

AC:

569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1444

2887

4331

5774

7218

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.227

Hom.:

6665

Bravo

AF:

0.282

Asia WGS

AF:

0.339

AC:

1180

AN:

3478

EpiCase

AF:

0.205

EpiControl

AF:

0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.17

(source)

DANN

Benign

0.57

PhyloP100

-1.3

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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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