18-11989970-G-A

Variant names:

• chr18-11989970-G-A
• rs650727
• NM_014214.3:c.96+8205G>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.96+8205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,008 control chromosomes in the GnomAD database, including 12,284 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 0.38 (12284 hom., cov: 32)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.96+8205G>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.96+8205G>A		intron_variant	Intron 1 of 7	1	NM_014214.3	ENSP00000269159.3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57501 AN: 151890 Hom.: 12246 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.379 AC: 57601 AN: 152008 Hom.: 12284 Cov.: 32 AF XY: 0.384 AC XY: 28510 AN XY: 74302

African (AFR) AF: 0.551 AC: 22861 AN: 41454

American (AMR) AF: 0.321 AC: 4905 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3147 AN: 5146

South Asian (SAS) AF: 0.485 AC: 2330 AN: 4804

European-Finnish (FIN) AF: 0.297 AC: 3149 AN: 10590

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19184 AN: 67944

Other (OTH) AF: 0.351 AC: 739 AN: 2108

Alfa AF: 0.353 Hom.: 1314

Bravo AF: 0.386

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.24
DANN	Benign	0.36
PhyloP100		-1.1
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: rs650727; hg19: chr18-11989969;