rs276229

chr10-104322178-A-Gchr10-104322178-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPRIP	NM_001272013.2	c.-13-6114T>C		intron_variant		ENST00000337478.3
ITPRIP	NM_001272012.2	c.-13-6114T>C		intron_variant
ITPRIP	NM_033397.4	c.-13-6114T>C		intron_variant
ITPRIP	XM_005270257.3	c.2+6076T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPRIP	ENST00000337478.3	c.-13-6114T>C		intron_variant		1	NM_001272013.2	P1

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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0241

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0714 Hom.: 153

Bravo AF: 0.121

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.38
Dann	Benign	0.89

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

Publications

LitVar

Other links and lift over

dbSNP: rs276229; hg19: chr10-106081936;