dbSNP rs2269996: PARP12:c.*2C>T (chr7-140024558-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_022750.4(PARP12):c.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 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
NM_022750.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

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:

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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=-0.91).

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	XM_047420739.1 link	c.*2C>T	3_prime_UTR_variant	Exon 12 of 12		XP_047276695.1
PARP12	NR_130117.2 link	n.2070C>T	non_coding_transcript_exon_variant	Exon 11 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP12	ENST00000263549 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

GnomAD3 exomes

AF:

0.263

AC:

65991

AN:

250768

Hom.:

10848

AF XY:

0.249

AC XY:

33804

AN XY:

135584

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 SAS exome

AF:

0.153

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

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.425

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.573

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.174

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.220

GnomAD4 genome

AF:

0.257

AC:

39056

AN:

152084

Hom.:

5724

Cov.:

AF XY:

0.257

AC XY:

19086

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.366

Gnomad4 ASJ

AF:

0.182

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.158

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.222

Hom.:

5109

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

DANN

Benign

0.57

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