Variant rs78411303 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001113523.3(PARP15):c.*1504G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,010 control chromosomes in the GnomAD database, including 284 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 0.054 ( 284 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

PARP15
NM_001113523.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.234

Variant links:

Genes affected

PARP15 (HGNC:26876): (poly(ADP-ribose) polymerase family member 15) Enables NAD+ binding activity; pentosyltransferase activity; and transcription corepressor activity. Involved in negative regulation of transcription by RNA polymerase II; protein mono-ADP-ribosylation; and protein poly-ADP-ribosylation. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PARP15 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARP15	NM_001113523.3 linkuse as main transcript	c.*1504G>A		3_prime_UTR_variant	12/12	ENST00000464300.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP15	ENST00000464300.7 linkuse as main transcript	c.*1504G>A		3_prime_UTR_variant	12/12	1	NM_001113523.3	P1	Q460N3-1
PARP15	ENST00000483793.5 linkuse as main transcript	c.*1504G>A		3_prime_UTR_variant	9/9	1

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8216

AN:

151892

Hom.:

281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.0824

Gnomad AMR

AF:

0.0662

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.0235

Gnomad SAS

AF:

0.0498

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0646

Gnomad OTH

AF:

0.0660

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.0541

AC:

8220

AN:

152010

Hom.:

284

Cov.:

AF XY:

0.0569

AC XY:

4230

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.0127

Gnomad4 AMR

AF:

0.0667

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.0236

Gnomad4 SAS

AF:

0.0494

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.0646

Gnomad4 OTH

AF:

0.0649

Alfa

AF:

0.0598

Hom.:

Bravo

AF:

0.0488

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.0

DANN

Benign

0.16

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over