3-156679960-C-T

Variant names:

• chr3-156679960-C-T
• rs2665390
• NM_015508.5:c.917+1346C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 44 publications found

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]

TIPARP-AS1 (HGNC:41028): (TIPARP antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015508.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIPARP	NM_015508.5	MANE Select	c.917+1346C>T		intron	N/A	NP_056323.2
	TIPARP	NM_001184717.1		c.917+1346C>T		intron	N/A	NP_001171646.1
	TIPARP	NM_001184718.2		c.917+1346C>T		intron	N/A	NP_001171647.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIPARP	ENST00000295924.12	TSL:1 MANE Select	c.917+1346C>T		intron	N/A	ENSP00000295924.7
	TIPARP	ENST00000461166.5	TSL:1	c.917+1346C>T		intron	N/A	ENSP00000420612.1
	TIPARP	ENST00000542783.5	TSL:1	c.917+1346C>T		intron	N/A	ENSP00000438345.1

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

African (AFR) AF: 0.913 AC: 37928 AN: 41528

American (AMR) AF: 0.949 AC: 14514 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3312 AN: 3472

East Asian (EAS) AF: 0.963 AC: 5002 AN: 5192

South Asian (SAS) AF: 0.902 AC: 4353 AN: 4828

European-Finnish (FIN) AF: 0.871 AC: 9221 AN: 10586

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62496 AN: 68018

Other (OTH) AF: 0.938 AC: 1980 AN: 2112

Alfa AF: 0.921 Hom.: 243492

Bravo AF: 0.927

Asia WGS AF: 0.896 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.65
PhyloP100		0.68
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: rs2665390; hg19: chr3-156397749;