rs78411303

Variant names:

• chr3-122637604-G-A
• rs78411303
• NM_001113523.3:c.*1504G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-122637604-G-A
• chr3-122637604-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARP15	NM_001113523.3	c.*1504G>A		3_prime_UTR_variant	Exon 12 of 12	ENST00000464300.7	NP_001106995.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP15	ENST00000464300.7	c.*1504G>A		3_prime_UTR_variant	Exon 12 of 12	1	NM_001113523.3	ENSP00000417214.2
PARP15	ENST00000483793.5	c.*1504G>A		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000417785.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0127 AC: 528 AN: 41456

American (AMR) AF: 0.0667 AC: 1018 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3468

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5170

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4814

European-Finnish (FIN) AF: 0.125 AC: 1319 AN: 10532

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4389 AN: 67990

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0582 Hom.: 556

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
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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