rs630110

Variant names:

• chr18-12029858-A-G
• rs630110
• NM_014214.3:c.752-485A>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.752-485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,210 control chromosomes in the GnomAD database, including 44,371 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 0.76 (44371 hom., cov: 33)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.70
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMPA2	NM_014214.3	MANE Select	c.752-485A>G		intron	N/A	NP_055029.1	O14732-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMPA2	ENST00000269159.8	TSL:1 MANE Select	c.752-485A>G		intron	N/A	ENSP00000269159.3	O14732-1
	IMPA2	ENST00000886600.1		c.491-485A>G		intron	N/A	ENSP00000556659.1
	IMPA2	ENST00000922526.1		c.488-485A>G		intron	N/A	ENSP00000592585.1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115649 AN: 152092 Hom.: 44334 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.760 AC: 115741 AN: 152210 Hom.: 44371 Cov.: 33 AF XY: 0.761 AC XY: 56655 AN XY: 74414

African (AFR) AF: 0.821 AC: 34092 AN: 41548

American (AMR) AF: 0.808 AC: 12358 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4736 AN: 5166

South Asian (SAS) AF: 0.735 AC: 3545 AN: 4826

European-Finnish (FIN) AF: 0.702 AC: 7427 AN: 10586

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48509 AN: 67994

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.734 Hom.: 33555

Bravo AF: 0.773

Asia WGS AF: 0.818 AC: 2846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.057
DANN	Benign	0.32
PhyloP100		-5.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs630110; hg19: chr18-12029857;