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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446672.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP4P2	ENST00000446672.2	TSL:6	n.2353T>C		non_coding_transcript_exon	Exon 18 of 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

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3929856;

hg19: chr13-19969056;