rs711631

Positions:

• chr3-4814496-T-A
• chr3-4814496-T-C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001378452.1(ITPR1):​c.7635T>A​(p.Thr2545Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T2545T) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITPR1 NM_001378452.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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]

ENSG00000235978 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP7: Synonymous conserved (PhyloP=-1.33 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.7635T>A	p.Thr2545Thr	synonymous_variant	58/62	ENST00000649015.2	NP_001365381.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.7635T>A	p.Thr2545Thr	synonymous_variant	58/62		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.7611T>A	p.Thr2537Thr	synonymous_variant	58/62	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.7608T>A	p.Thr2536Thr	synonymous_variant	58/62			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.7593T>A	p.Thr2531Thr	synonymous_variant	57/61			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.7590T>A	p.Thr2530Thr	synonymous_variant	57/61	1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.7563T>A	p.Thr2521Thr	synonymous_variant	55/59			ENSP00000497026.1
ITPR1	ENST00000357086.10	c.7491T>A	p.Thr2497Thr	synonymous_variant	55/59	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.7446T>A	p.Thr2482Thr	synonymous_variant	54/58	1		ENSP00000397885.2
ITPR1	ENST00000648038.1	c.5397T>A	p.Thr1799Thr	synonymous_variant	38/42			ENSP00000497872.1
ITPR1	ENST00000648431.1	c.4812T>A	p.Thr1604Thr	synonymous_variant	35/39			ENSP00000498149.1
ITPR1	ENST00000648212.1	c.4575T>A	p.Thr1525Thr	synonymous_variant	35/39			ENSP00000498022.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461590 Hom.: 0 Cov.: 44 AF XY: 0.00 AC XY: 0 AN XY: 727076

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.42
DANN	Benign	0.83

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: rs711631; hg19: chr3-4856180;