10-87505267-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The ENST00000371996.9(MINPP1):​c.352G>A​(p.Gly118Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

MINPP1
ENST00000371996.9 missense

Scores

1
18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0270
Variant links:
Genes affected
MINPP1 (HGNC:7102): (multiple inositol-polyphosphate phosphatase 1) This gene encodes multiple inositol polyphosphate phosphatase; an enzyme that removes 3-phosphate from inositol phosphate substrates. It is the only enzyme known to hydrolzye inositol pentakisphosphate and inositol hexakisphosphate. This enzyme also converts 2,3 bisphosphoglycerate (2,3-BPG) to 2-phosphoglycerate; an activity formerly thought to be exclusive to 2,3-BPG synthase/2-phosphatase (BPGM) in the Rapoport-Luebering shunt of the glycolytic pathway.[provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06981301).
BP6
Variant 10-87505267-G-A is Benign according to our data. Variant chr10-87505267-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2258143.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MINPP1NM_004897.5 linkuse as main transcriptc.352G>A p.Gly118Arg missense_variant 1/5 ENST00000371996.9 NP_004888.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MINPP1ENST00000371996.9 linkuse as main transcriptc.352G>A p.Gly118Arg missense_variant 1/51 NM_004897.5 ENSP00000361064 P1Q9UNW1-1
MINPP1ENST00000371994.8 linkuse as main transcriptc.352G>A p.Gly118Arg missense_variant 1/31 ENSP00000361062 Q9UNW1-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000809
AC:
2
AN:
247172
Hom.:
0
AF XY:
0.00000745
AC XY:
1
AN XY:
134236
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000581
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1459122
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
725394
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsOct 29, 2021This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
0.59
DANN
Benign
0.74
DEOGEN2
Benign
0.077
T;.
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.012
N
LIST_S2
Benign
0.54
T;T
M_CAP
Benign
0.062
D
MetaRNN
Benign
0.070
T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
0.48
N;N
MutationTaster
Benign
1.0
N;N
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-0.35
N;N
REVEL
Benign
0.12
Sift
Benign
0.32
T;T
Sift4G
Benign
0.24
T;T
Polyphen
0.0
B;B
Vest4
0.031
MutPred
0.41
Gain of MoRF binding (P = 0.0073);Gain of MoRF binding (P = 0.0073);
MVP
0.40
MPC
0.46
ClinPred
0.051
T
GERP RS
-5.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.4
Varity_R
0.055
gMVP
0.55

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: rs1427501545; hg19: chr10-89265024; API