rs78411303

chr3-122637604-G-Achr3-122637604-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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]

ACMG classification

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	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	c.*1504G>A		3_prime_UTR_variant	12/12	1	NM_001113523.3	P1
PARP15	ENST00000483793.5	c.*1504G>A		3_prime_UTR_variant	9/9	1

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8216 AN: 151892 Hom.: 281 Cov.: 32

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: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0541 AC: 8220 AN: 152010 Hom.: 284 Cov.: 32 AF XY: 0.0569 AC XY: 4230 AN XY: 74292

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.: 77

Bravo AF: 0.0488

Asia WGS AF: 0.0240 AC: 84 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

Other links and lift over

dbSNP: rs78411303; hg19: chr3-122356451; COSMIC: COSV59971480; COSMIC: COSV59971480;