rs650727

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014214.3(IMPA2):​c.96+8205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,008 control chromosomes in the GnomAD database, including 12,284 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 0.38 ( 12284 hom., cov: 32)

Consequence

IMPA2
NM_014214.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IMPA2NM_014214.3 linkuse as main transcriptc.96+8205G>A intron_variant ENST00000269159.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IMPA2ENST00000269159.8 linkuse as main transcriptc.96+8205G>A intron_variant 1 NM_014214.3 P1O14732-1

Frequencies

GnomAD3 genomes
AF:
0.379
AC:
57501
AN:
151890
Hom.:
12246
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.551
Gnomad AMI
AF:
0.354
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.611
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.297
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.282
Gnomad OTH
AF:
0.350
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57601
AN:
152008
Hom.:
12284
Cov.:
32
AF XY:
0.384
AC XY:
28510
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.551
Gnomad4 AMR
AF:
0.321
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.612
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.297
Gnomad4 NFE
AF:
0.282
Gnomad4 OTH
AF:
0.351
Alfa
AF:
0.345
Hom.:
1193
Bravo
AF:
0.386
Asia WGS
AF:
0.552
AC:
1919
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
0.24
DANN
Benign
0.36

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs650727; hg19: chr18-11989969; API