chr3-156700967-C-T

Position:

• chr3-156700967-C-T

Variant summary

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

The NM_015508.5(TIPARP):​c.1248-2457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,230 control chromosomes in the GnomAD database, including 1,298 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 0.12 (1298 hom., cov: 32)
• Consequence: TIPARP NM_015508.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TIPARP	NM_015508.5	c.1248-2457C>T		intron_variant		ENST00000295924.12
TIPARP	NM_001184717.1	c.1248-2457C>T		intron_variant
TIPARP	NM_001184718.2	c.1248-2457C>T		intron_variant
TIPARP	XM_047447935.1	c.1248-2457C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TIPARP	ENST00000295924.12	c.1248-2457C>T		intron_variant		1	NM_015508.5	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18176 AN: 152110 Hom.: 1298 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.120 AC: 18192 AN: 152230 Hom.: 1298 Cov.: 32 AF XY: 0.117 AC XY: 8687 AN XY: 74430

Gnomad4 AFR AF: 0.0392

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.120

Alfa AF: 0.153 Hom.: 2359

Bravo AF: 0.118

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.67
DANN	Benign	0.87

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: rs1367311; hg19: chr3-156418756;