rs78411303

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

2

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]

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=-0.96).
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
PARP15NM_001113523.3 linkuse as main transcriptc.*1504G>A 3_prime_UTR_variant 12/12 ENST00000464300.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PARP15ENST00000464300.7 linkuse as main transcriptc.*1504G>A 3_prime_UTR_variant 12/121 NM_001113523.3 P1Q460N3-1
PARP15ENST00000483793.5 linkuse as main transcriptc.*1504G>A 3_prime_UTR_variant 9/91

Frequencies

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

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

Other links and lift over

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