12-26300350-A-G

Variant names:

• chr12-26300350-A-G
• rs718314
• ENST00000540392.1:n.130+26034T>C

Variant summary

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

The ENST00000540392.1(ITPR2-AS1):​n.130+26034T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,918 control chromosomes in the GnomAD database, including 6,805 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 0.28 (6805 hom., cov: 32)
• Consequence: ITPR2-AS1 ENST00000540392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 110 publications found

Genes affected

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

ENSG00000255750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369705	XR_007063249.1	n.991-773A>G		intron_variant	Intron 3 of 5
LOC105369705	XR_931451.3	n.991-773A>G		intron_variant	Intron 3 of 4
LOC105369705	XR_931452.3	n.990+1925A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR2-AS1	ENST00000540392.1	n.130+26034T>C		intron_variant	Intron 2 of 3	3
ENSG00000255750	ENST00000540625.5	n.119+19252T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41797 AN: 151800 Hom.: 6796 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.275 AC: 41834 AN: 151918 Hom.: 6805 Cov.: 32 AF XY: 0.281 AC XY: 20856 AN XY: 74240

African (AFR) AF: 0.201 AC: 8304 AN: 41406

American (AMR) AF: 0.455 AC: 6954 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3464

East Asian (EAS) AF: 0.697 AC: 3605 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3094 AN: 10524

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17051 AN: 67948

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.269 Hom.: 28806

Bravo AF: 0.287

Asia WGS AF: 0.412 AC: 1432 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.31
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs718314; hg19: chr12-26453283;