chr13-19389783-G-A

Variant names:

• chr13-19389783-G-A
• rs17080801

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 0.0664 in 152,062 control chromosomes in the GnomAD database, including 402 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 0.066 (402 hom., cov: 32)
• Consequence: PARP4P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP4P2	ENST00000446672.2	TSL:6	n.1825+1918G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10104 AN: 151944 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0664 AC: 10104 AN: 152062 Hom.: 402 Cov.: 32 AF XY: 0.0674 AC XY: 5007 AN XY: 74310

African (AFR) AF: 0.0395 AC: 1638 AN: 41460

American (AMR) AF: 0.0625 AC: 955 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.165 AC: 850 AN: 5154

South Asian (SAS) AF: 0.151 AC: 728 AN: 4818

European-Finnish (FIN) AF: 0.0507 AC: 535 AN: 10556

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0704 AC: 4789 AN: 68016

Other (OTH) AF: 0.0882 AC: 186 AN: 2110

Alfa AF: 0.0228 Hom.: 15

Bravo AF: 0.0631

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.53
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17080801; hg19: chr13-19963923;