12-26539038-C-T

Position:

• chr12-26539038-C-T

Variant summary

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

The NM_002223.4(ITPR2):​c.5073+11209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,084 control chromosomes in the GnomAD database, including 28,274 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 0.57 (28274 hom., cov: 33)
• Consequence: ITPR2 NM_002223.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPR2	NM_002223.4	c.5073+11209G>A		intron_variant		ENST00000381340.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPR2	ENST00000381340.8	c.5073+11209G>A		intron_variant		1	NM_002223.4	P1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86018 AN: 151964 Hom.: 28273 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.566 AC: 86033 AN: 152084 Hom.: 28274 Cov.: 33 AF XY: 0.562 AC XY: 41765 AN XY: 74348

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.580

Alfa AF: 0.662 Hom.: 4397

Bravo AF: 0.530

Asia WGS AF: 0.425 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.42

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: rs4414322; hg19: chr12-26691971;