rs2322734

Positions:

• chr3-4591808-C-A
• chr3-4591808-C-G
• chr3-4591808-C-T

Variant summary

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

The NM_001378452.1(ITPR1):​c.164-35955C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,248 control chromosomes in the GnomAD database, including 64,882 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 0.92 (64882 hom., cov: 32)
• Consequence: ITPR1 NM_001378452.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

ITPR1 (HGNC:6180): (inositol 1,4,5-trisphosphate receptor type 1) This gene encodes an intracellular receptor for inositol 1,4,5-trisphosphate. Upon stimulation by inositol 1,4,5-trisphosphate, this receptor mediates calcium release from the endoplasmic reticulum. Mutations in this gene cause spinocerebellar ataxia type 15, a disease associated with an heterogeneous group of cerebellar disorders. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.164-35955C>A		intron_variant		ENST00000649015.2	NP_001365381.1
ITPR1	NM_001099952.4	c.164-35955C>A		intron_variant			NP_001093422.2
ITPR1	NM_001168272.2	c.164-35955C>A		intron_variant			NP_001161744.1
ITPR1	NM_002222.7	c.164-35955C>A		intron_variant			NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.164-35955C>A		intron_variant			NM_001378452.1	ENSP00000497605

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140200 AN: 152130 Hom.: 64820 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.922 AC: 140321 AN: 152248 Hom.: 64882 Cov.: 32 AF XY: 0.921 AC XY: 68551 AN XY: 74426

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.962

Gnomad4 ASJ AF: 0.994

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.943

Alfa AF: 0.958 Hom.: 48415

Bravo AF: 0.921

Asia WGS AF: 0.888 AC: 3084 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.73

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: rs2322734; hg19: chr3-4633492;