rs2058350

Positions:

• chr12-3804261-C-T

Variant summary

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

The variant allele was found at a frequency of 0.226 in 151,956 control chromosomes in the GnomAD database, including 4,327 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 0.23 (4327 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

(HGNC:):

PARP11 (HGNC:1186): (poly(ADP-ribose) polymerase family member 11) Enables NAD+ ADP-ribosyltransferase activity and protein ADP-ribosylase activity. Involved in protein auto-ADP-ribosylation and protein mono-ADP-ribosylation. Located in cytosol; nuclear body; and nuclear envelope. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.3804261C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARP11	ENST00000416739.5	n.*196+2627G>A		intron_variant		2		ENSP00000392392.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34286 AN: 151838 Hom.: 4321 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34320 AN: 151956 Hom.: 4327 Cov.: 31 AF XY: 0.228 AC XY: 16964 AN XY: 74296

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.242

Alfa AF: 0.201 Hom.: 1872

Bravo AF: 0.240

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2058350; hg19: chr12-3913427;