rs3929856

chr13-19394916-T-C

Variant summary

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

The ENST00000446672.2(PARP4P2):n.2353T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 958,114 control chromosomes in the GnomAD database, including 31,844 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 0.31 (8309 hom., cov: 31)
  • Exomes 𝑓: 0.23 (23535 hom.)
• Consequence: PARP4P2 ENST00000446672.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

PARP4P2 (HGNC:37760): (poly(ADP-ribose) polymerase family member 4 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP4P2	ENST00000446672.2	n.2353T>C		non_coding_transcript_exon_variant	18/21

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46477 AN: 151690 Hom.: 8274 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.324

GnomAD4 exome AF: 0.231 AC: 186619 AN: 806304 Hom.: 23535 Cov.: 11 AF XY: 0.234 AC XY: 96216 AN XY: 411930

Gnomad4 AFR exome AF: 0.487

Gnomad4 AMR exome AF: 0.217

Gnomad4 ASJ exome AF: 0.392

Gnomad4 EAS exome AF: 0.0706

Gnomad4 SAS exome AF: 0.269

Gnomad4 FIN exome AF: 0.183

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.307 AC: 46578 AN: 151810 Hom.: 8309 Cov.: 31 AF XY: 0.301 AC XY: 22368 AN XY: 74212

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0958

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.330

Alfa AF: 0.269 Hom.: 1301

Bravo AF: 0.319

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.71
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3929856; hg19: chr13-19969056;