NM_001378452.1:c.5103+2427G>A

Variant names:

• chr3-4714295-G-A
• rs722368
• NM_001378452.1:c.5103+2427G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378452.1(ITPR1):​c.5103+2427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,992 control chromosomes in the GnomAD database, including 25,033 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 0.56 (25033 hom., cov: 32)
• Consequence: ITPR1 NM_001378452.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 4 publications found

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]

ITPR1 Gene-Disease associations (from GenCC):

• aniridia-cerebellar ataxia-intellectual disability syndrome

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Genomics England PanelApp, PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• spinocerebellar ataxia type 29

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet
• spinocerebellar ataxia type 15/16

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.5103+2427G>A		intron_variant	Intron 39 of 61	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.5058+2427G>A		intron_variant	Intron 38 of 60		NP_001161744.1
ITPR1	NM_001099952.4	c.5076+2427G>A		intron_variant	Intron 39 of 58		NP_001093422.2
ITPR1	NM_002222.7	c.5031+2427G>A		intron_variant	Intron 38 of 57		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.5103+2427G>A		intron_variant	Intron 39 of 61		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.5076+2427G>A		intron_variant	Intron 39 of 61	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.5076+2427G>A		intron_variant	Intron 39 of 61			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.5058+2427G>A		intron_variant	Intron 38 of 60			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.5058+2427G>A		intron_variant	Intron 38 of 60	1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.5031+2427G>A		intron_variant	Intron 36 of 58			ENSP00000497026.1
ITPR1	ENST00000357086.10	c.5076+2427G>A		intron_variant	Intron 39 of 58	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.5031+2427G>A		intron_variant	Intron 38 of 57	1		ENSP00000397885.2
ITPR1	ENST00000648038.1	c.2913+2427G>A		intron_variant	Intron 20 of 41			ENSP00000497872.1
ITPR1	ENST00000648431.1	c.2403+2427G>A		intron_variant	Intron 17 of 38			ENSP00000498149.1
ITPR1	ENST00000648212.1	c.2010+2427G>A		intron_variant	Intron 15 of 38			ENSP00000498022.1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85691 AN: 151876 Hom.: 24996 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.564 AC: 85792 AN: 151992 Hom.: 25033 Cov.: 32 AF XY: 0.555 AC XY: 41229 AN XY: 74304

African (AFR) AF: 0.545 AC: 22605 AN: 41456

American (AMR) AF: 0.530 AC: 8102 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.184 AC: 953 AN: 5168

South Asian (SAS) AF: 0.355 AC: 1707 AN: 4808

European-Finnish (FIN) AF: 0.541 AC: 5712 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43330 AN: 67930

Other (OTH) AF: 0.520 AC: 1096 AN: 2108

Alfa AF: 0.606 Hom.: 86744

Bravo AF: 0.561

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs722368; hg19: chr3-4755979;