3-122685661-C-T

Variant names:

• chr3-122685661-C-T
• rs1272161
• NM_017554.3:c.321+343C>T

Variant summary

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

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARP14	NM_017554.3	c.321+343C>T		intron_variant	Intron 2 of 16	ENST00000474629.7	NP_060024.2
PARP14	XM_011512929.3	c.321+343C>T		intron_variant	Intron 2 of 9		XP_011511231.1
PARP14	XR_007095695.1	n.366+343C>T		intron_variant	Intron 2 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP14	ENST00000474629.7	c.321+343C>T		intron_variant	Intron 2 of 16	1	NM_017554.3	ENSP00000418194.2
PARP14	ENST00000494811.2	c.321+343C>T		intron_variant	Intron 2 of 3	4		ENSP00000418535.2
PARP14	ENST00000649945.1	n.321+343C>T		intron_variant	Intron 2 of 15			ENSP00000497854.1

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

African (AFR) AF: 0.581 AC: 24018 AN: 41356

American (AMR) AF: 0.393 AC: 6004 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2963 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2049 AN: 4808

European-Finnish (FIN) AF: 0.271 AC: 2849 AN: 10524

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14291 AN: 67932

Other (OTH) AF: 0.344 AC: 725 AN: 2108

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
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1272161; hg19: chr3-122404508;