rs6901411

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002224.4(ITPR3):​c.1410-85A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,488,066 control chromosomes in the GnomAD database, including 66,060 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4951 hom., cov: 32)
Exomes 𝑓: 0.30 ( 61109 hom. )

Consequence

ITPR3
NM_002224.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.667
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 6-33665750-A-G is Benign according to our data. Variant chr6-33665750-A-G is described in ClinVar as [Benign]. Clinvar id is 1293549.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITPR3NM_002224.4 linkuse as main transcriptc.1410-85A>G intron_variant ENST00000605930.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITPR3ENST00000605930.3 linkuse as main transcriptc.1410-85A>G intron_variant 1 NM_002224.4 P1
ITPR3ENST00000374316.9 linkuse as main transcriptc.1410-85A>G intron_variant 5 P1

Frequencies

GnomAD3 genomes
AF:
0.242
AC:
36794
AN:
151866
Hom.:
4948
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.133
Gnomad AMI
AF:
0.343
Gnomad AMR
AF:
0.234
Gnomad ASJ
AF:
0.171
Gnomad EAS
AF:
0.438
Gnomad SAS
AF:
0.400
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.230
GnomAD4 exome
AF:
0.296
AC:
395953
AN:
1336082
Hom.:
61109
AF XY:
0.300
AC XY:
198898
AN XY:
663932
show subpopulations
Gnomad4 AFR exome
AF:
0.129
Gnomad4 AMR exome
AF:
0.243
Gnomad4 ASJ exome
AF:
0.173
Gnomad4 EAS exome
AF:
0.437
Gnomad4 SAS exome
AF:
0.399
Gnomad4 FIN exome
AF:
0.303
Gnomad4 NFE exome
AF:
0.294
Gnomad4 OTH exome
AF:
0.285
GnomAD4 genome
AF:
0.242
AC:
36819
AN:
151984
Hom.:
4951
Cov.:
32
AF XY:
0.247
AC XY:
18326
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.133
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.438
Gnomad4 SAS
AF:
0.401
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.230
Alfa
AF:
0.266
Hom.:
4691
Bravo
AF:
0.232
Asia WGS
AF:
0.408
AC:
1417
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 12, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.64

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: rs6901411; hg19: chr6-33633527; COSMIC: COSV65412842; API