rs589247

chr18-11992726-T-Cchr18-11992726-T-G

Variant summary

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

The NM_014214.3(IMPA2):c.97-6328T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,970 control chromosomes in the GnomAD database, including 13,107 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 0.39 (13107 hom., cov: 32)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMPA2	NM_014214.3	c.97-6328T>C		intron_variant		ENST00000269159.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMPA2	ENST00000269159.8	c.97-6328T>C		intron_variant		1	NM_014214.3	P1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58906 AN: 151852 Hom.: 13071 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.388 AC: 59006 AN: 151970 Hom.: 13107 Cov.: 32 AF XY: 0.392 AC XY: 29149 AN XY: 74284

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.361

Alfa AF: 0.324 Hom.: 2198

Bravo AF: 0.397

Asia WGS AF: 0.557 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.46

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: rs589247; hg19: chr18-11992725;