rs17080523

Variant names:

• chr13-19358398-T-C
• rs17080523

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.13 in 152,204 control chromosomes in the GnomAD database, including 1,567 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 0.13 (1567 hom., cov: 32)
• Consequence: PARP4P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP4P2		n.19358398T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP4P2	ENST00000446672.2	n.393+827T>C		intron_variant	Intron 4 of 20	6

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19748 AN: 152086 Hom.: 1558 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.130 AC: 19794 AN: 152204 Hom.: 1567 Cov.: 32 AF XY: 0.127 AC XY: 9484 AN XY: 74416

African (AFR) AF: 0.230 AC: 9565 AN: 41512

American (AMR) AF: 0.0858 AC: 1313 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3470

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5186

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.0562 AC: 595 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0935 AC: 6359 AN: 68008

Other (OTH) AF: 0.148 AC: 312 AN: 2108

Alfa AF: 0.107 Hom.: 439

Bravo AF: 0.135

Asia WGS AF: 0.167 AC: 580 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.91
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs17080523; hg19: chr13-19932538;