Variant 6-33640439-G-T 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.90-45G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,580,972 control chromosomes in the GnomAD database, including 12,374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 840 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11534 hom. )

Consequence

ITPR3
NM_002224.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.732

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=-0.87).

BP6

Variant 6-33640439-G-T is Benign according to our data. Variant chr6-33640439-G-T is described in ClinVar as [Benign]. Clinvar id is 1293544.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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.90-45G>T		intron_variant		ENST00000605930.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPR3	ENST00000605930.3 linkuse as main transcript	c.90-45G>T		intron_variant		1	NM_002224.4	P1
ITPR3	ENST00000374316.9 linkuse as main transcript	c.90-45G>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15508

AN:

152168

Hom.:

838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0917

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.0212

Gnomad SAS

AF:

0.0839

Gnomad FIN

AF:

0.0812

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0856

GnomAD3 exomes

AF:

0.101

AC:

23852

AN:

235190

Hom.:

1368

AF XY:

0.0999

AC XY:

12718

AN XY:

127294

show subpopulations

Gnomad AFR exome

AF:

0.0878

Gnomad AMR exome

AF:

0.134

Gnomad ASJ exome

AF:

0.0593

Gnomad EAS exome

AF:

0.0154

Gnomad SAS exome

AF:

0.0852

Gnomad FIN exome

AF:

0.0852

Gnomad NFE exome

AF:

0.119

Gnomad OTH exome

AF:

0.100

GnomAD4 exome

AF:

0.122

AC:

174935

AN:

1428686

Hom.:

11534

Cov.:

AF XY:

0.121

AC XY:

86028

AN XY:

711360

show subpopulations

Gnomad4 AFR exome

AF:

0.0797

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.0630

Gnomad4 EAS exome

AF:

0.0330

Gnomad4 SAS exome

AF:

0.0873

Gnomad4 FIN exome

AF:

0.0911

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.102

AC:

15518

AN:

152286

Hom.:

840

Cov.:

AF XY:

0.0986

AC XY:

7339

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0916

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.0212

Gnomad4 SAS

AF:

0.0836

Gnomad4 FIN

AF:

0.0812

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.0848

Alfa

AF:

0.107

Hom.:

305

Bravo

AF:

0.103

Asia WGS

AF:

0.0690

AC:

241

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

-0.87

CADD

Benign

3.2

DANN

Benign

0.74

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

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