rs11111201

chr12-102194697-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017915.5(PARPBP):c.1264-615G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,666 control chromosomes in the GnomAD database, including 1,776 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 0.15 (1776 hom., cov: 32)
• Consequence: PARPBP NM_017915.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

Genes affected

PARPBP (HGNC:26074): (PARP1 binding protein) Predicted to enable DNA binding activity. Involved in negative regulation of double-strand break repair via homologous recombination. Located in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARPBP	NM_017915.5	c.1264-615G>A		intron_variant		ENST00000327680.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARPBP	ENST00000327680.7	c.1264-615G>A		intron_variant		2	NM_017915.5	P1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22404 AN: 151546 Hom.: 1774 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.148 AC: 22420 AN: 151666 Hom.: 1776 Cov.: 32 AF XY: 0.147 AC XY: 10862 AN XY: 74098

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.145

Alfa AF: 0.161 Hom.: 670

Bravo AF: 0.138

Asia WGS AF: 0.146 AC: 507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs11111201; hg19: chr12-102588475;