rs3929856

Variant names:

• chr13-19394916-T-C
• rs3929856
• ENST00000446672.2:n.2353T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARP4P2		n.19394916T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP4P2	ENST00000446672.2	n.2353T>C		non_coding_transcript_exon_variant	Exon 18 of 21	6

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

African (AFR) AF: 0.487 AC: 8671 AN: 17808

American (AMR) AF: 0.217 AC: 5386 AN: 24808

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 6150 AN: 15678

East Asian (EAS) AF: 0.0706 AC: 2453 AN: 34760

South Asian (SAS) AF: 0.269 AC: 14133 AN: 52452

European-Finnish (FIN) AF: 0.183 AC: 8732 AN: 47826

Middle Eastern (MID) AF: 0.393 AC: 1060 AN: 2694

European-Non Finnish (NFE) AF: 0.227 AC: 130412 AN: 573250

Other (OTH) AF: 0.260 AC: 9622 AN: 37028

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

African (AFR) AF: 0.491 AC: 20278 AN: 41336

American (AMR) AF: 0.247 AC: 3767 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3468

East Asian (EAS) AF: 0.0958 AC: 491 AN: 5126

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4810

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16475 AN: 67930

Other (OTH) AF: 0.330 AC: 694 AN: 2106

Alfa AF: 0.270 Hom.: 2364

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3929856; hg19: chr13-19969056;