3-156689208-G-T

Position:

• chr3-156689208-G-T

Variant summary

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

The NM_015508.5(TIPARP):​c.918-4812G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,100 control chromosomes in the GnomAD database, including 660 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 0.075 (660 hom., cov: 32)
• Consequence: TIPARP NM_015508.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

Genes affected

TIPARP (HGNC:23696): (TCDD inducible poly(ADP-ribose) polymerase) This gene encodes a member of the poly(ADP-ribose) polymerase superfamily. Studies of the mouse ortholog have shown that the encoded protein catalyzes histone poly(ADP-ribosyl)ation and may be involved in T-cell function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TIPARP	NM_015508.5	c.918-4812G>T		intron_variant		ENST00000295924.12
TIPARP	NM_001184717.1	c.918-4812G>T		intron_variant
TIPARP	NM_001184718.2	c.918-4812G>T		intron_variant
TIPARP	XM_047447935.1	c.918-4812G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TIPARP	ENST00000295924.12	c.918-4812G>T		intron_variant		1	NM_015508.5	P1

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11422 AN: 151982 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00664

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0484

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0752 AC: 11435 AN: 152100 Hom.: 660 Cov.: 32 AF XY: 0.0739 AC XY: 5494 AN XY: 74378

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00664

Gnomad4 FIN AF: 0.0728

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0533 Hom.: 154

Bravo AF: 0.0774

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.53

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: rs7651446; hg19: chr3-156406997;