12-26331042-C-T

Variant names:

• chr12-26331042-C-T
• rs7976877
• ENST00000535324.1:n.52+12038C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000535324.1(ENSG00000255968):​n.52+12038C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,848 control chromosomes in the GnomAD database, including 12,230 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 0.40 (12230 hom., cov: 31)
• Consequence: ENSG00000255968 ENST00000535324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 3 publications found

Genes affected

ENSG00000255968 (HGNC:58268):

ITPR2-AS1 (HGNC:56072): (ITPR2 and SSPN antisense RNA 1)

LOC107984482 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR2-AS2	NR_199072.1	n.81+12038C>T		intron_variant	Intron 1 of 5
LOC107984482	XR_001749054.2	n.280+744G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255968	ENST00000535324.1	n.52+12038C>T		intron_variant	Intron 1 of 5	3
ITPR2-AS1	ENST00000540392.1	n.38-4566G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60345 AN: 151732 Hom.: 12215 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.398 AC: 60393 AN: 151848 Hom.: 12230 Cov.: 31 AF XY: 0.396 AC XY: 29397 AN XY: 74190

African (AFR) AF: 0.439 AC: 18189 AN: 41400

American (AMR) AF: 0.489 AC: 7459 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5158

South Asian (SAS) AF: 0.276 AC: 1326 AN: 4808

European-Finnish (FIN) AF: 0.400 AC: 4204 AN: 10520

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24524 AN: 67924

Other (OTH) AF: 0.369 AC: 777 AN: 2108

Alfa AF: 0.266 Hom.: 697

Bravo AF: 0.406

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.50
PhyloP100		-0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7976877; hg19: chr12-26483975;