NM_001042618.2:c.1102-51G>T

Variant names:

• chr14-20356256-G-T
• rs3093933
• NM_001042618.2:c.1102-51G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.20 (3659 hom., cov: 32)
  • Exomes 𝑓: 0.25 (45512 hom.)
• Consequence: PARP2 NM_001042618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 23 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042618.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP2	NM_001042618.2	MANE Select	c.1102-51G>T		intron	N/A	NP_001036083.1
	PARP2	NM_005484.4		c.1141-51G>T		intron	N/A	NP_005475.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP2	ENST00000429687.8	TSL:1 MANE Select	c.1102-51G>T		intron	N/A	ENSP00000392972.3
	PARP2	ENST00000250416.9	TSL:1	c.1141-51G>T		intron	N/A	ENSP00000250416.5
	PARP2	ENST00000925416.1		c.1126-51G>T		intron	N/A	ENSP00000595475.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30993 AN: 151920 Hom.: 3660 Cov.: 32

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

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.: 30 AF XY: 0.250 AC XY: 179464 AN XY: 718924

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

GnomAD4 genome AF: 0.204 AC: 30996 AN: 152036 Hom.: 3659 Cov.: 32 AF XY: 0.205 AC XY: 15255 AN XY: 74288

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: 53 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16752 AN: 67978

Other (OTH) AF: 0.207 AC: 438 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.41
PhyloP100		0.35
PromoterAI		-0.014	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3093933; hg19: chr14-20824415; COSMIC: COSV51639476; COSMIC: COSV51639476;