rs73807272

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001378452.1(ITPR1):​c.92+29C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 1,241,180 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

ITPR1
NM_001378452.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.139
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITPR1NM_001378452.1 linkc.92+29C>A intron_variant Intron 3 of 61 ENST00000649015.2 NP_001365381.1
ITPR1NM_001168272.2 linkc.92+29C>A intron_variant Intron 3 of 60 NP_001161744.1 Q14643-2
ITPR1NM_001099952.4 linkc.92+29C>A intron_variant Intron 3 of 58 NP_001093422.2 Q14643-3B4DER3Q59H91
ITPR1NM_002222.7 linkc.92+29C>A intron_variant Intron 3 of 57 NP_002213.5 Q14643-4B4DER3B4DGH1Q59H91

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITPR1ENST00000649015.2 linkc.92+29C>A intron_variant Intron 3 of 61 NM_001378452.1 ENSP00000497605.1 Q14643-1
ITPR1ENST00000354582.12 linkc.92+29C>A intron_variant Intron 3 of 61 5 ENSP00000346595.8 A0A3F2YNW8
ITPR1ENST00000648266.1 linkc.92+29C>A intron_variant Intron 3 of 61 ENSP00000498014.1 A0A3B3IU04
ITPR1ENST00000650294.1 linkc.92+29C>A intron_variant Intron 3 of 60 ENSP00000498056.1 A0A3B3ITU8
ITPR1ENST00000443694.5 linkc.92+29C>A intron_variant Intron 3 of 60 1 ENSP00000401671.2 Q14643-2
ITPR1ENST00000648309.1 linkc.92+29C>A intron_variant Intron 1 of 58 ENSP00000497026.1 Q14643-5
ITPR1ENST00000357086.10 linkc.92+29C>A intron_variant Intron 3 of 58 1 ENSP00000349597.4 Q14643-3
ITPR1ENST00000456211.8 linkc.92+29C>A intron_variant Intron 3 of 57 1 ENSP00000397885.2 Q14643-4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000161
AC:
2
AN:
1241180
Hom.:
0
Cov.:
17
AF XY:
0.00000319
AC XY:
2
AN XY:
627774
show subpopulations
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:
0.00000217
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
3.1
DANN
Benign
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73807272; hg19: chr3-4558296; API