rs6872889

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024615.4(PARP8):​c.146+19284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0234 in 152,268 control chromosomes in the GnomAD database, including 140 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 0.023 ( 140 hom., cov: 32)

Consequence

PARP8
NM_024615.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.340
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0794 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PARP8NM_024615.4 linkuse as main transcriptc.146+19284A>G intron_variant ENST00000281631.10 NP_078891.2 Q8N3A8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PARP8ENST00000281631.10 linkuse as main transcriptc.146+19284A>G intron_variant 1 NM_024615.4 ENSP00000281631.4 Q8N3A8-1

Frequencies

GnomAD3 genomes
AF:
0.0232
AC:
3528
AN:
152150
Hom.:
137
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0812
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00576
Gnomad ASJ
AF:
0.00374
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000382
Gnomad OTH
AF:
0.0167
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0234
AC:
3557
AN:
152268
Hom.:
140
Cov.:
32
AF XY:
0.0222
AC XY:
1653
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0817
Gnomad4 AMR
AF:
0.00569
Gnomad4 ASJ
AF:
0.00374
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000382
Gnomad4 OTH
AF:
0.0166
Alfa
AF:
0.0207
Hom.:
9
Bravo
AF:
0.0264
Asia WGS
AF:
0.0110
AC:
39
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
9.3
DANN
Benign
0.84

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6872889; hg19: chr5-49983243; API