NM_002223.4:c.5074-12143A>G

Variant names:

• chr12-26507403-T-C
• rs16930911
• NM_002223.4:c.5074-12143A>G

Variant summary

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

The NM_002223.4(ITPR2):​c.5074-12143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,272 control chromosomes in the GnomAD database, including 1,220 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 0.078 (1220 hom., cov: 32)
• Consequence: ITPR2 NM_002223.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

Genes affected

ITPR2 (HGNC:6181): (inositol 1,4,5-trisphosphate receptor type 2) The protein encoded by this gene belongs to the inositol 1,4,5-triphosphate receptor family, whose members are second messenger intracellular calcium release channels. These proteins mediate a rise in cytoplasmic calcium in response to receptor activated production of inositol triphosphate. Inositol triphosphate receptor-mediated signaling is involved in many processes including cell migration, cell division, smooth muscle contraction, and neuronal signaling. This protein is a type 2 receptor that consists of a cytoplasmic amino-terminus that binds inositol triphosphate, six membrane-spanning helices that contribute to the ion pore, and a short cytoplasmic carboxy-terminus. A mutation in this gene has been associated with anhidrosis, suggesting that intracellular calcium release mediated by this protein is required for eccrine sweat production. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR2	NM_002223.4	c.5074-12143A>G		intron_variant	Intron 37 of 56	ENST00000381340.8	NP_002214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR2	ENST00000381340.8	c.5074-12143A>G		intron_variant	Intron 37 of 56	1	NM_002223.4	ENSP00000370744.3

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11873 AN: 152154 Hom.: 1218 Cov.: 32

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0780 AC: 11878 AN: 152272 Hom.: 1220 Cov.: 32 AF XY: 0.0841 AC XY: 6264 AN XY: 74440

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0896

Gnomad4 NFE AF: 0.0459

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0894 Hom.: 229

Bravo AF: 0.0919

Asia WGS AF: 0.245 AC: 849 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.61

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: rs16930911; hg19: chr12-26660336;