Variant rs2296337 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002224.4(ITPR3):c.1148+39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,609,442 control chromosomes in the GnomAD database, including 69,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4866 hom., cov: 32)

Exomes 𝑓: 0.29 ( 64994 hom. )

Consequence

ITPR3
NM_002224.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.61

Variant links:

Genes affected

ITPR3 (HGNC:6182): (inositol 1,4,5-trisphosphate receptor type 3) This gene encodes a receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium. The receptor contains a calcium channel at the C-terminus and the ligand-binding site at the N-terminus. Knockout studies in mice suggest that type 2 and type 3 inositol 1,4,5-trisphosphate receptors play a key role in exocrine secretion underlying energy metabolism and growth. [provided by RefSeq, Aug 2010]

ITPR3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 6-33663919-G-A is Benign according to our data. Variant chr6-33663919-G-A is described in ClinVar as [Benign]. Clinvar id is 1269800.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPR3	NM_002224.4 linkuse as main transcript	c.1148+39G>A		intron_variant		ENST00000605930.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPR3	ENST00000605930.3 linkuse as main transcript	c.1148+39G>A		intron_variant		1	NM_002224.4	P1
ITPR3	ENST00000374316.9 linkuse as main transcript	c.1148+39G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36574

AN:

151944

Hom.:

4863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.225

GnomAD3 exomes

AF:

0.286

AC:

70648

AN:

247188

Hom.:

10695

AF XY:

0.294

AC XY:

39252

AN XY:

133678

show subpopulations

Gnomad AFR exome

AF:

0.133

Gnomad AMR exome

AF:

0.246

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.381

Gnomad FIN exome

AF:

0.298

Gnomad NFE exome

AF:

0.279

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.294

AC:

427826

AN:

1457380

Hom.:

64994

Cov.:

AF XY:

0.296

AC XY:

214483

AN XY:

724776

show subpopulations

Gnomad4 AFR exome

AF:

0.132

Gnomad4 AMR exome

AF:

0.241

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.437

Gnomad4 SAS exome

AF:

0.378

Gnomad4 FIN exome

AF:

0.302

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.282

GnomAD4 genome

AF:

0.241

AC:

36598

AN:

152062

Hom.:

4866

Cov.:

AF XY:

0.245

AC XY:

18186

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.234

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.435

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.277

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.269

Hom.:

3626

Bravo

AF:

0.231

Asia WGS

AF:

0.396

AC:

1376

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.7

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over