3-4654962-T-C

Position:

• chr3-4654962-T-C

Variant summary

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

The NM_001378452.1(ITPR1):​c.996+1076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,914 control chromosomes in the GnomAD database, including 18,534 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 0.49 (18534 hom., cov: 31)
• Consequence: ITPR1 NM_001378452.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.996+1076T>C		intron_variant		ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.951+2744T>C		intron_variant			NP_001161744.1
ITPR1	NM_001099952.4	c.996+1076T>C		intron_variant			NP_001093422.2
ITPR1	NM_002222.7	c.951+2744T>C		intron_variant			NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.996+1076T>C		intron_variant			NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.996+1076T>C		intron_variant		5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.996+1076T>C		intron_variant				ENSP00000498014.1
ITPR1	ENST00000650294.1	c.951+2744T>C		intron_variant				ENSP00000498056.1
ITPR1	ENST00000443694.5	c.951+2744T>C		intron_variant		1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.951+2744T>C		intron_variant				ENSP00000497026.1
ITPR1	ENST00000357086.10	c.996+1076T>C		intron_variant		1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.951+2744T>C		intron_variant		1		ENSP00000397885.2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73591 AN: 151796 Hom.: 18499 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.485 AC: 73692 AN: 151914 Hom.: 18534 Cov.: 31 AF XY: 0.480 AC XY: 35652 AN XY: 74254

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.504

Alfa AF: 0.442 Hom.: 22755

Bravo AF: 0.501

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.68

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: rs17709863; hg19: chr3-4696646;