3-156679960-C-T

Position:

• chr3-156679960-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.917+1346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,232 control chromosomes in the GnomAD database, including 64,363 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 0.92 (64363 hom., cov: 31)
• Consequence: TIPARP NM_015508.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TIPARP	NM_015508.5	c.917+1346C>T		intron_variant		ENST00000295924.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TIPARP	ENST00000295924.12	c.917+1346C>T		intron_variant		1	NM_015508.5	P1

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139878 AN: 152114 Hom.: 64330 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.919 AC: 139960 AN: 152232 Hom.: 64363 Cov.: 31 AF XY: 0.918 AC XY: 68321 AN XY: 74434

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.938

Alfa AF: 0.923 Hom.: 113543

Bravo AF: 0.927

Asia WGS AF: 0.896 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.65

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: rs2665390; hg19: chr3-156397749;