rs669838

chr18-11994599-C-A

Variant summary

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

The NM_014214.3(IMPA2):c.97-4455C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,076 control chromosomes in the GnomAD database, including 17,817 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 0.46 (17817 hom., cov: 33)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMPA2	NM_014214.3	c.97-4455C>A		intron_variant		ENST00000269159.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMPA2	ENST00000269159.8	c.97-4455C>A		intron_variant		1	NM_014214.3	P1
	ENST00000592820.1	n.143+197G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69287 AN: 151958 Hom.: 17783 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.456 AC: 69385 AN: 152076 Hom.: 17817 Cov.: 33 AF XY: 0.459 AC XY: 34074 AN XY: 74302

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.450

Alfa AF: 0.357 Hom.: 16579

Bravo AF: 0.467

Asia WGS AF: 0.587 AC: 2042 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	1.3
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs669838; hg19: chr18-11994598;