chr10-104322178-A-G

Variant names:

• chr10-104322178-A-G
• rs276229
• NM_001272013.2:c.-13-6114T>C

Variant summary

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

The NM_001272013.2(ITPRIP):​c.-13-6114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,052 control chromosomes in the GnomAD database, including 1,996 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 0.11 (1996 hom., cov: 32)
• Consequence: ITPRIP NM_001272013.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 1 publications found

Genes affected

ITPRIP (HGNC:29370): (inositol 1,4,5-trisphosphate receptor interacting protein) This gene encodes a membrane-associated protein that binds the inositol 1,4,5-trisphosphate receptor (ITPR). The encoded protein enhances the sensitivity of ITPR to intracellular calcium signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

ITPRIP-AS1 (HGNC:54100): (ITPRIP antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001272013.2. 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
	ITPRIP	NM_001272013.2	MANE Select	c.-13-6114T>C		intron	N/A	NP_001258942.1
	ITPRIP	NM_001272012.2		c.-13-6114T>C		intron	N/A	NP_001258941.1
	ITPRIP	NM_033397.4		c.-13-6114T>C		intron	N/A	NP_203755.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITPRIP	ENST00000337478.3	TSL:1 MANE Select	c.-13-6114T>C		intron	N/A	ENSP00000337178.1
	ITPRIP	ENST00000278071.6	TSL:1	c.-13-6114T>C		intron	N/A	ENSP00000278071.2
	ITPRIP	ENST00000458723.1	TSL:1	c.-13-6114T>C		intron	N/A	ENSP00000414141.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16554 AN: 151934 Hom.: 1990 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0834

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

GnomAD4 genome AF: 0.109 AC: 16592 AN: 152052 Hom.: 1996 Cov.: 32 AF XY: 0.108 AC XY: 8053 AN XY: 74322

African (AFR) AF: 0.300 AC: 12410 AN: 41370

American (AMR) AF: 0.0554 AC: 847 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.118 AC: 613 AN: 5174

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4820

European-Finnish (FIN) AF: 0.0402 AC: 427 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1642 AN: 68006

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0639 Hom.: 267

Bravo AF: 0.121

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.38
DANN	Benign	0.89
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs276229; hg19: chr10-106081936;