18-11987273-C-T

Variant names:

• chr18-11987273-C-T
• rs7506045
• NM_014214.3:c.96+5508C>T

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+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
• Publications: 22 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=-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 rank	MANE	Protein	UniProt
IMPA2	NM_014214.3	c.96+5508C>T		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+5508C>T		intron_variant	Intron 1 of 7	1	NM_014214.3	ENSP00000269159.3

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

African (AFR) AF: 0.121 AC: 5007 AN: 41532

American (AMR) AF: 0.170 AC: 2600 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1455 AN: 5192

South Asian (SAS) AF: 0.0925 AC: 445 AN: 4810

European-Finnish (FIN) AF: 0.102 AC: 1086 AN: 10612

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4886 AN: 68012

Other (OTH) AF: 0.0963 AC: 203 AN: 2108

Alfa AF: 0.0859 Hom.: 3174

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
PhyloP100		-1.2
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: rs7506045; hg19: chr18-11987272;