3-156688610-A-G

Variant names:

• chr3-156688610-A-G
• rs344008
• NM_015508.5:c.918-5410A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015508.5(TIPARP):​c.918-5410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,028 control chromosomes in the GnomAD database, including 59,173 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 0.88 (59173 hom., cov: 29)
• Consequence: TIPARP NM_015508.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 7 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=-0.8).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIPARP	NM_015508.5	MANE Select	c.918-5410A>G		intron	N/A	NP_056323.2
	TIPARP	NM_001184717.1		c.918-5410A>G		intron	N/A	NP_001171646.1
	TIPARP	NM_001184718.2		c.918-5410A>G		intron	N/A	NP_001171647.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIPARP	ENST00000295924.12	TSL:1 MANE Select	c.918-5410A>G		intron	N/A	ENSP00000295924.7
	TIPARP	ENST00000461166.5	TSL:1	c.918-5410A>G		intron	N/A	ENSP00000420612.1
	TIPARP	ENST00000542783.5	TSL:1	c.918-5410A>G		intron	N/A	ENSP00000438345.1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133670 AN: 151910 Hom.: 59144 Cov.: 29

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.949

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.880 AC: 133746 AN: 152028 Hom.: 59173 Cov.: 29 AF XY: 0.880 AC XY: 65345 AN XY: 74292

African (AFR) AF: 0.775 AC: 32086 AN: 41424

American (AMR) AF: 0.937 AC: 14307 AN: 15268

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

East Asian (EAS) AF: 0.963 AC: 4976 AN: 5166

South Asian (SAS) AF: 0.902 AC: 4346 AN: 4820

European-Finnish (FIN) AF: 0.870 AC: 9187 AN: 10558

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

European-Non Finnish (NFE) AF: 0.918 AC: 62459 AN: 68006

Other (OTH) AF: 0.910 AC: 1921 AN: 2110

Alfa AF: 0.902 Hom.: 43081

Bravo AF: 0.882

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		1.9
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: rs344008; hg19: chr3-156406399;