chr12-3804261-C-T

Variant names:

• chr12-3804261-C-T
• rs2058350
• ENST00000416739.5:n.*196+2627G>A

Variant summary

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

The ENST00000416739.5(PARP11):​n.*196+2627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: PARP11 ENST00000416739.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP11	ENST00000416739.5	n.*196+2627G>A		intron_variant	Intron 8 of 9	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;