18-11996338-G-A

Variant names:

• chr18-11996338-G-A
• rs636173
• NM_014214.3:c.97-2716G>A

Variant summary

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

The NM_014214.3(IMPA2):​c.97-2716G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,000 control chromosomes in the GnomAD database, including 18,878 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 0.47 (18878 hom., cov: 32)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.97-2716G>A		intron_variant	Intron 1 of 7	ENST00000269159.8	NP_055029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMPA2	ENST00000269159.8	c.97-2716G>A		intron_variant	Intron 1 of 7	1	NM_014214.3	ENSP00000269159.3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70887 AN: 151882 Hom.: 18836 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.467 AC: 70994 AN: 152000 Hom.: 18878 Cov.: 32 AF XY: 0.469 AC XY: 34851 AN XY: 74300

African (AFR) AF: 0.717 AC: 29705 AN: 41418

American (AMR) AF: 0.399 AC: 6090 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3195 AN: 5160

South Asian (SAS) AF: 0.537 AC: 2592 AN: 4828

European-Finnish (FIN) AF: 0.330 AC: 3487 AN: 10574

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.340 AC: 23109 AN: 67976

Other (OTH) AF: 0.458 AC: 967 AN: 2112

Alfa AF: 0.380 Hom.: 6851

Bravo AF: 0.479

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.55
PhyloP100		-0.89
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: rs636173; hg19: chr18-11996337;