rs166863

Variant names:

• chr5-50741617-A-G
• rs166863
• NM_024615.4:c.147-8534A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-50741617-A-G
• chr5-50741617-A-T

Variant summary

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

The NM_024615.4(PARP8):​c.147-8534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,926 control chromosomes in the GnomAD database, including 23,557 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 0.54 (23557 hom., cov: 31)
• Consequence: PARP8 NM_024615.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 2 publications found

Genes affected

PARP8 (HGNC:26124): (poly(ADP-ribose) polymerase family member 8) Enables protein ADP-ribosylase activity. Involved in protein auto-ADP-ribosylation and protein mono-ADP-ribosylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP8	NM_024615.4	c.147-8534A>G		intron_variant	Intron 2 of 25	ENST00000281631.10	NP_078891.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP8	ENST00000281631.10	c.147-8534A>G		intron_variant	Intron 2 of 25	1	NM_024615.4	ENSP00000281631.4

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81282 AN: 151808 Hom.: 23550 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.535 AC: 81291 AN: 151926 Hom.: 23557 Cov.: 31 AF XY: 0.537 AC XY: 39913 AN XY: 74276

African (AFR) AF: 0.301 AC: 12457 AN: 41420

American (AMR) AF: 0.585 AC: 8927 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3464

East Asian (EAS) AF: 0.644 AC: 3337 AN: 5182

South Asian (SAS) AF: 0.449 AC: 2168 AN: 4824

European-Finnish (FIN) AF: 0.693 AC: 7294 AN: 10524

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43098 AN: 67934

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.543 Hom.: 3482

Bravo AF: 0.521

Asia WGS AF: 0.510 AC: 1775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.40
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs166863; hg19: chr5-50037451;