rs17080523

Positions:

• chr13-19358398-T-C

Variant summary

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

The ENST00000446672.2(PARP4P2):​n.393+827T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 ENST00000446672.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

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=-0.85).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP4P2	ENST00000446672.2	n.393+827T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0935

Gnomad4 OTH AF: 0.148

Alfa AF: 0.106 Hom.: 364

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17080523; hg19: chr13-19932538;