rs3786282

Positions:

• chr18-12013183-A-C
• chr18-12013183-A-T

Variant summary

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

The NM_014214.3(IMPA2):​c.381+968A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,892 control chromosomes in the GnomAD database, including 12,518 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 (12518 hom., cov: 31)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.381+968A>C		intron_variant		ENST00000269159.8	NP_055029.1
IMPA2	XM_011525659.4	c.333+968A>C		intron_variant			XP_011523961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMPA2	ENST00000269159.8	c.381+968A>C		intron_variant		1	NM_014214.3	ENSP00000269159	P1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58657 AN: 151772 Hom.: 12492 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.387 AC: 58739 AN: 151892 Hom.: 12518 Cov.: 31 AF XY: 0.388 AC XY: 28818 AN XY: 74238

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.375

Alfa AF: 0.357 Hom.: 2401

Bravo AF: 0.404

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.44

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: rs3786282; hg19: chr18-12013182;