18-11987273-C-T

Position:

• chr18-11987273-C-T

Variant summary

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

The NM_014214.3(IMPA2):​c.96+5508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,224 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 33)
• Consequence: IMPA2 NM_014214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.96+5508C>T		intron_variant		ENST00000269159.8	NP_055029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMPA2	ENST00000269159.8	c.96+5508C>T		intron_variant		1	NM_014214.3	ENSP00000269159	P1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16076 AN: 152106 Hom.: 1031 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.106 AC: 16109 AN: 152224 Hom.: 1040 Cov.: 33 AF XY: 0.109 AC XY: 8106 AN XY: 74418

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.0963

Alfa AF: 0.0854 Hom.: 1660

Bravo AF: 0.113

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.80

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: rs7506045; hg19: chr18-11987272;