chr6-33655156-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002224.4(ITPR3):c.161-610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,102 control chromosomes in the GnomAD database, including 3,754 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 0.20 ( 3754 hom., cov: 32)
Consequence
ITPR3
NM_002224.4 intron
NM_002224.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.52
Publications
15 publications found
Genes affected
ITPR3 (HGNC:6182): (inositol 1,4,5-trisphosphate receptor type 3) This gene encodes a receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium. The receptor contains a calcium channel at the C-terminus and the ligand-binding site at the N-terminus. Knockout studies in mice suggest that type 2 and type 3 inositol 1,4,5-trisphosphate receptors play a key role in exocrine secretion underlying energy metabolism and growth. [provided by RefSeq, Aug 2010]
ITPR3 Gene-Disease associations (from GenCC):
- Charcot-Marie-Tooth disease, demyelinating, type 1JInheritance: AD Classification: DEFINITIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.202 AC: 30717AN: 151984Hom.: 3757 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
30717
AN:
151984
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.202 AC: 30712AN: 152102Hom.: 3754 Cov.: 32 AF XY: 0.210 AC XY: 15607AN XY: 74334 show subpopulations
GnomAD4 genome
AF:
AC:
30712
AN:
152102
Hom.:
Cov.:
32
AF XY:
AC XY:
15607
AN XY:
74334
show subpopulations
African (AFR)
AF:
AC:
2607
AN:
41532
American (AMR)
AF:
AC:
3879
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
984
AN:
3472
East Asian (EAS)
AF:
AC:
1449
AN:
5166
South Asian (SAS)
AF:
AC:
1411
AN:
4812
European-Finnish (FIN)
AF:
AC:
3702
AN:
10556
Middle Eastern (MID)
AF:
AC:
59
AN:
292
European-Non Finnish (NFE)
AF:
AC:
16035
AN:
67986
Other (OTH)
AF:
AC:
364
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1162
2324
3486
4648
5810
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
332
664
996
1328
1660
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
762
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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