3-122685661-C-T

Variant summary

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

The NM_017554.3(PARP14):c.321+343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,822 control chromosomes in the GnomAD database, including 11,694 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 0.36 (11694 hom., cov: 30)
• Consequence: PARP14 NM_017554.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

PARP14 (HGNC:29232): (poly(ADP-ribose) polymerase family member 14) This gene encodes a member of the poly(ADP-ribose) polymerase (PARP) protein family. The encoded anti-apoptotic protein may regulate aerobic glycolysis and promote survival of cancer cells. Increased expression of this gene has been reported in a variety of tumor types. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARP14	NM_017554.3	c.321+343C>T		intron_variant		ENST00000474629.7
PARP14	XM_011512929.3	c.321+343C>T		intron_variant
PARP14	XR_007095695.1	n.366+343C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARP14	ENST00000474629.7	c.321+343C>T		intron_variant		1	NM_017554.3	P1
PARP14	ENST00000494811.2	c.321+343C>T		intron_variant		4
PARP14	ENST00000649945.1	c.321+343C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54003 AN: 151702 Hom.: 11663 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.356 AC: 54091 AN: 151822 Hom.: 11694 Cov.: 30 AF XY: 0.361 AC XY: 26823 AN XY: 74204

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.344

Alfa AF: 0.288 Hom.: 936

Bravo AF: 0.376

Asia WGS AF: 0.469 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.9
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1272161; hg19: chr3-122404508;