Genetic Variant PARP15:c.*1504G>T (chr3-122637604-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001113523.3(PARP15):c.*1504G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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

Publications

0 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001113523.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PARP15	NM_001113523.3	MANE Select	c.*1504G>T	3_prime_UTR	Exon 12 of 12	NP_001106995.1
PARP15	NM_001308320.2		c.*1504G>T	3_prime_UTR	Exon 9 of 9	NP_001295249.1
PARP15	NM_152615.3		c.*1504G>T	3_prime_UTR	Exon 8 of 8	NP_689828.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP15	ENST00000464300.7	TSL:1 MANE Select	c.*1504G>T		3_prime_UTR	Exon 12 of 12	ENSP00000417214.2
	PARP15	ENST00000483793.5	TSL:1	c.*1504G>T		3_prime_UTR	Exon 9 of 9	ENSP00000417785.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

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American (AMR)

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Ashkenazi Jewish (ASJ)

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East Asian (EAS)

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South Asian (SAS)

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European-Finnish (FIN)

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Middle Eastern (MID)

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European-Non Finnish (NFE)

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Other (OTH)

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GnomAD4 genome

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ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.40

(source)

DANN

Benign

0.18

PhyloP100

-0.23

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over