rs1027089

Positions:

• chr12-26318137-C-G

Variant summary

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

The ENST00000540392.1(ITPR2-AS1):​n.130+8247G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,118 control chromosomes in the GnomAD database, including 9,175 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 0.32 (9175 hom., cov: 33)
• Consequence: ITPR2-AS1 ENST00000540392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITPR2-AS1	ENST00000540392.1	n.130+8247G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000540625.5	n.119+1465G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49267 AN: 152000 Hom.: 9178 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.324 AC: 49276 AN: 152118 Hom.: 9175 Cov.: 33 AF XY: 0.325 AC XY: 24136 AN XY: 74346

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.344

Alfa AF: 0.352 Hom.: 1254

Bravo AF: 0.305

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1027089; hg19: chr12-26471070;