rs1020294

Variant names:

• chr18-12017344-A-G
• rs1020294
• NM_014214.3:c.490+2971A>G

Variant summary

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

The NM_014214.3(IMPA2):​c.490+2971A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,024 control chromosomes in the GnomAD database, including 17,239 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 0.45 (17239 hom., cov: 32)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 5 publications found

Genes affected

IMPA2 (HGNC:6051): (inositol monophosphatase 2) This locus encodes an inositol monophosphatase. The encoded protein catalyzes the dephosphoylration of inositol monophosphate and plays an important role in phosphatidylinositol signaling. This locus may be associated with susceptibility to bipolar disorder. [provided by RefSeq, Jan 2011]

ENSG00000293189 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.490+2971A>G		intron_variant	Intron 5 of 7	ENST00000269159.8	NP_055029.1
IMPA2	XM_011525659.4	c.442+2971A>G		intron_variant	Intron 4 of 6		XP_011523961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMPA2	ENST00000269159.8	c.490+2971A>G		intron_variant	Intron 5 of 7	1	NM_014214.3	ENSP00000269159.3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67654 AN: 151906 Hom.: 17239 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.445 AC: 67679 AN: 152024 Hom.: 17239 Cov.: 32 AF XY: 0.441 AC XY: 32765 AN XY: 74292

African (AFR) AF: 0.233 AC: 9667 AN: 41486

American (AMR) AF: 0.406 AC: 6199 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2080 AN: 3468

East Asian (EAS) AF: 0.150 AC: 778 AN: 5172

South Asian (SAS) AF: 0.312 AC: 1502 AN: 4808

European-Finnish (FIN) AF: 0.591 AC: 6237 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39528 AN: 67958

Other (OTH) AF: 0.501 AC: 1056 AN: 2106

Alfa AF: 0.535 Hom.: 101336

Bravo AF: 0.426

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1020294; hg19: chr18-12017343;