chr5-50730631-C-T

Position:

• chr5-50730631-C-T

Variant summary

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

The NM_024615.4(PARP8):​c.147-19520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,926 control chromosomes in the GnomAD database, including 23,308 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 0.53 (23308 hom., cov: 32)
• Consequence: PARP8 NM_024615.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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/exons	MANE	UniProt
PARP8	NM_024615.4	c.147-19520C>T		intron_variant		ENST00000281631.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP8	ENST00000281631.10	c.147-19520C>T		intron_variant		1	NM_024615.4	P1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80481 AN: 151808 Hom.: 23302 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.530 AC: 80489 AN: 151926 Hom.: 23308 Cov.: 32 AF XY: 0.532 AC XY: 39516 AN XY: 74226

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.557

Alfa AF: 0.615 Hom.: 58535

Bravo AF: 0.515

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs282544; hg19: chr5-50026465;