GeneBe

rs1038639

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001378452.1(ITPR1):​c.93-41T>A variant causes a intron change. 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.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ITPR1
NM_001378452.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.22

Publications

19 publications found
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]
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)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378452.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ITPR1
NM_001378452.1
MANE Select
c.93-41T>A
intron
N/ANP_001365381.1
ITPR1
NM_001168272.2
c.93-41T>A
intron
N/ANP_001161744.1
ITPR1
NM_001099952.4
c.93-41T>A
intron
N/ANP_001093422.2

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ITPR1
ENST00000649015.2
MANE Select
c.93-41T>A
intron
N/AENSP00000497605.1
ITPR1
ENST00000354582.12
TSL:5
c.93-41T>A
intron
N/AENSP00000346595.8
ITPR1
ENST00000648266.1
c.93-41T>A
intron
N/AENSP00000498014.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1326482
Hom.:
0
Cov.:
19
AF XY:
0.00
AC XY:
0
AN XY:
667432
African (AFR)
AF:
0.00
AC:
0
AN:
30996
American (AMR)
AF:
0.00
AC:
0
AN:
44174
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25198
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38932
South Asian (SAS)
AF:
0.00
AC:
0
AN:
83348
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53164
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5508
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
989348
Other (OTH)
AF:
0.00
AC:
0
AN:
55814
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
12
DANN
Benign
0.86
PhyloP100
4.2

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

Other links and lift over

dbSNP: rs1038639; hg19: chr3-4562667; API