Variant 6-33655732-T-C 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.161-34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 1,613,086 control chromosomes in the GnomAD database, including 2,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.050 ( 222 hom., cov: 32)

Exomes 𝑓: 0.047 ( 1841 hom. )

Consequence

ITPR3
NM_002224.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.323

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=-0.93).

BP6

Variant 6-33655732-T-C is Benign according to our data. Variant chr6-33655732-T-C is described in ClinVar as [Benign]. Clinvar id is 1270368.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.068 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.161-34T>C		intron_variant		ENST00000605930.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPR3	ENST00000605930.3 linkuse as main transcript	c.161-34T>C		intron_variant		1	NM_002224.4	P1
ITPR3	ENST00000374316.9 linkuse as main transcript	c.161-34T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.0497

AC:

7550

AN:

152034

Hom.:

220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0698

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0383

Gnomad ASJ

AF:

0.0439

Gnomad EAS

AF:

0.00828

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.0199

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0507

Gnomad OTH

AF:

0.0511

GnomAD3 exomes

AF:

0.0371

AC:

9257

AN:

249548

Hom.:

247

AF XY:

0.0356

AC XY:

4806

AN XY:

135014

show subpopulations

Gnomad AFR exome

AF:

0.0683

Gnomad AMR exome

AF:

0.0249

Gnomad ASJ exome

AF:

0.0434

Gnomad EAS exome

AF:

0.0113

Gnomad SAS exome

AF:

0.0145

Gnomad FIN exome

AF:

0.0217

Gnomad NFE exome

AF:

0.0489

Gnomad OTH exome

AF:

0.0405

GnomAD4 exome

AF:

0.0468

AC:

68311

AN:

1460934

Hom.:

1841

Cov.:

AF XY:

0.0453

AC XY:

32895

AN XY:

726688

show subpopulations

Gnomad4 AFR exome

AF:

0.0660

Gnomad4 AMR exome

AF:

0.0283

Gnomad4 ASJ exome

AF:

0.0411

Gnomad4 EAS exome

AF:

0.00695

Gnomad4 SAS exome

AF:

0.0145

Gnomad4 FIN exome

AF:

0.0212

Gnomad4 NFE exome

AF:

0.0524

Gnomad4 OTH exome

AF:

0.0434

GnomAD4 genome

AF:

0.0498

AC:

7573

AN:

152152

Hom.:

222

Cov.:

AF XY:

0.0478

AC XY:

3554

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0702

Gnomad4 AMR

AF:

0.0383

Gnomad4 ASJ

AF:

0.0439

Gnomad4 EAS

AF:

0.00830

Gnomad4 SAS

AF:

0.0139

Gnomad4 FIN

AF:

0.0199

Gnomad4 NFE

AF:

0.0507

Gnomad4 OTH

AF:

0.0506

Alfa

AF:

0.0489

Hom.:

Bravo

AF:

0.0527

Asia WGS

AF:

0.0140

AC:

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

-0.93

CADD

Benign

8.2

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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