6-33666859-C-T

Variant names:

• chr6-33666859-C-T
• rs9357163
• NM_002224.4:c.1552-270C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002224.4(ITPR3):​c.1552-270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,152 control chromosomes in the GnomAD database, including 51,658 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 0.82 (51658 hom., cov: 32)
• Consequence: ITPR3 NM_002224.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR3	NM_002224.4	c.1552-270C>T		intron_variant	Intron 14 of 57	ENST00000605930.3	NP_002215.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR3	ENST00000605930.3	c.1552-270C>T		intron_variant	Intron 14 of 57	1	NM_002224.4	ENSP00000475177.1
ITPR3	ENST00000374316.9	c.1552-270C>T		intron_variant	Intron 15 of 58	5		ENSP00000363435.4

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125087 AN: 152034 Hom.: 51611 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.823 AC: 125189 AN: 152152 Hom.: 51658 Cov.: 32 AF XY: 0.827 AC XY: 61505 AN XY: 74400

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.814

Alfa AF: 0.828 Hom.: 6502

Bravo AF: 0.812

Asia WGS AF: 0.897 AC: 3121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.88

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

Other links and lift over

dbSNP: rs9357163; hg19: chr6-33634636;