Variant rs2295283 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021933.4(MIIP):c.499A>G(p.Lys167Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 1,607,932 control chromosomes in the GnomAD database, including 403,825 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.72 ( 40164 hom., cov: 30)

Exomes 𝑓: 0.70 ( 363661 hom. )

Consequence

MIIP
NM_021933.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.41

Variant links:

Genes affected

MIIP (HGNC:25715): (migration and invasion inhibitory protein) This gene encodes a protein that interacts with the oncogene protein insulin-like growth factor binding protein 2 and may function as an inhibitor of cell migration and invasion. This protein also interacts with the cell division protein 20 and may be involved in regulating mitotic progression. This protein may function as a tumor suppressor by inhibiting the growth or certain cancers. [provided by RefSeq, Sep 2011]

MIIP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.370722E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MIIP	NM_021933.4 linkuse as main transcript	c.499A>G	p.Lys167Glu	missense_variant	4/10	ENST00000235332.6
MIIP	XM_011541895.2 linkuse as main transcript	c.499A>G	p.Lys167Glu	missense_variant	4/10
MIIP	XM_011541896.2 linkuse as main transcript	c.499A>G	p.Lys167Glu	missense_variant	4/10
MIIP	XM_005263487.5 linkuse as main transcript	c.499A>G	p.Lys167Glu	missense_variant	4/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIIP	ENST00000235332.6 linkuse as main transcript	c.499A>G	p.Lys167Glu	missense_variant	4/10	1	NM_021933.4	P1	Q5JXC2-1
MIIP	ENST00000466860.5 linkuse as main transcript	n.258A>G		non_coding_transcript_exon_variant	2/6	5
MIIP	ENST00000478749.5 linkuse as main transcript	n.472A>G		non_coding_transcript_exon_variant	3/6	2
MIIP	ENST00000498685.5 linkuse as main transcript	n.6A>G		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109616

AN:

151866

Hom.:

40125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.826

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.721

Gnomad OTH

AF:

0.703

GnomAD3 exomes

AF:

0.682

AC:

165360

AN:

242416

Hom.:

57370

AF XY:

0.681

AC XY:

89221

AN XY:

130948

show subpopulations

Gnomad AFR exome

AF:

0.792

Gnomad AMR exome

AF:

0.567

Gnomad ASJ exome

AF:

0.609

Gnomad EAS exome

AF:

0.552

Gnomad SAS exome

AF:

0.628

Gnomad FIN exome

AF:

0.823

Gnomad NFE exome

AF:

0.718

Gnomad OTH exome

AF:

0.689

GnomAD4 exome

AF:

0.704

AC:

1024873

AN:

1455948

Hom.:

363661

Cov.:

AF XY:

0.702

AC XY:

508047

AN XY:

723830

show subpopulations

Gnomad4 AFR exome

AF:

0.785

Gnomad4 AMR exome

AF:

0.576

Gnomad4 ASJ exome

AF:

0.607

Gnomad4 EAS exome

AF:

0.502

Gnomad4 SAS exome

AF:

0.633

Gnomad4 FIN exome

AF:

0.820

Gnomad4 NFE exome

AF:

0.716

Gnomad4 OTH exome

AF:

0.697

GnomAD4 genome

AF:

0.722

AC:

109722

AN:

151984

Hom.:

40164

Cov.:

AF XY:

0.721

AC XY:

53561

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.786

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.605

Gnomad4 EAS

AF:

0.552

Gnomad4 SAS

AF:

0.632

Gnomad4 FIN

AF:

0.826

Gnomad4 NFE

AF:

0.721

Gnomad4 OTH

AF:

0.702

Alfa

AF:

0.704

Hom.:

96005

Bravo

AF:

0.708

TwinsUK

AF:

0.716

AC:

2654

ALSPAC

AF:

0.715

AC:

2755

ESP6500AA

AF:

0.785

AC:

3459

ESP6500EA

AF:

0.714

AC:

6143

ExAC

AF:

0.684

AC:

82955

Asia WGS

AF:

0.596

AC:

2076

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.048

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.73

DEOGEN2

Benign

0.00049

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0064

LIST_S2

Benign

0.11

MetaRNN

Benign

9.4e-7

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.5

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.34

PROVEAN

Benign

1.8

REVEL

Benign

0.049

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.0030

MPC

0.13

ClinPred

0.00025

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.032

gMVP

0.11

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over