3-4516490-A-G

Variant names:

• chr3-4516490-A-G
• rs369723935
• NM_001378452.1:c.-2A>G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Moderate BP6 BS1

The NM_001378452.1(ITPR1):​c.-2A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000374 in 1,551,514 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00039 (1 hom.)
• Consequence: ITPR1 NM_001378452.1 5_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:2
• Conservation: PhyloP100: 1.19

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 -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BP6: Variant 3-4516490-A-G is Benign according to our data. Variant chr3-4516490-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 345337.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1, Likely_benign=1}.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000203 (31/152340) while in subpopulation NFE AF= 0.000338 (23/68022). AF 95% confidence interval is 0.00023. There are 0 homozygotes in gnomad4. There are 9 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.-2A>G		5_prime_UTR_variant	Exon 3 of 62	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.-2A>G		5_prime_UTR_variant	Exon 3 of 61		NP_001161744.1
ITPR1	NM_001099952.4	c.-2A>G		5_prime_UTR_variant	Exon 3 of 59		NP_001093422.2
ITPR1	NM_002222.7	c.-2A>G		5_prime_UTR_variant	Exon 3 of 58		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015	c.-2A>G		5_prime_UTR_variant	Exon 3 of 62		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582	c.-2A>G		5_prime_UTR_variant	Exon 3 of 62	5		ENSP00000346595.8
ITPR1	ENST00000648266	c.-2A>G		5_prime_UTR_variant	Exon 3 of 62			ENSP00000498014.1
ITPR1	ENST00000650294	c.-2A>G		5_prime_UTR_variant	Exon 3 of 61			ENSP00000498056.1
ITPR1	ENST00000443694	c.-2A>G		5_prime_UTR_variant	Exon 3 of 61	1		ENSP00000401671.2
ITPR1	ENST00000648309	c.-2A>G		5_prime_UTR_variant	Exon 1 of 59			ENSP00000497026.1
ITPR1	ENST00000357086	c.-2A>G		5_prime_UTR_variant	Exon 3 of 59	1		ENSP00000349597.4
ITPR1	ENST00000456211	c.-2A>G		5_prime_UTR_variant	Exon 3 of 58	1		ENSP00000397885.2

Frequencies

GnomAD3 genomes AF: 0.000204 AC: 31 AN: 152222 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000338

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000419 AC: 93 AN: 221952 Hom.: 0 AF XY: 0.000338 AC XY: 41 AN XY: 121216

Gnomad AFR exome AF: 0.0000736

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000399

Gnomad FIN exome AF: 0.0000472

Gnomad NFE exome AF: 0.000839

Gnomad OTH exome AF: 0.000379

GnomAD4 exome AF: 0.000392 AC: 549 AN: 1399174 Hom.: 1 Cov.: 25 AF XY: 0.000359 AC XY: 250 AN XY: 696920

Gnomad4 AFR exome AF: 0.0000647

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000129

Gnomad4 FIN exome AF: 0.000150

Gnomad4 NFE exome AF: 0.000473

Gnomad4 OTH exome AF: 0.000533

GnomAD4 genome AF: 0.000203 AC: 31 AN: 152340 Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9 AN XY: 74496

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.000338

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000198 Hom.: 0

Bravo AF: 0.000136

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1

Mar 17, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nucleotide substitution has no predicted effect on splicing and is not conserved across species; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 29758065) -

not specified Benign:1

May 06, 2020

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal dominant cerebellar ataxia Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.89
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs369723935; hg19: chr3-4558174;