Variant 1-1615612-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001170687.4(MIB2):c.-151C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,569,886 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0014 ( 1 hom., cov: 34)

Exomes 𝑓: 0.0012 ( 12 hom. )

Consequence

MIB2
NM_001170687.4 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.758

Variant links:

Genes affected

MIB2 (HGNC:30577): (MIB E3 ubiquitin protein ligase 2) The protein encoded by this gene is an E3 ubiquitin protein ligase that mediates ubiquitination of proteins in the Notch signaling pathway. The encoded protein may be a suppressor of melanoma invasion. [provided by RefSeq, Mar 2017]

MIB2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_addAF=-0.352183).

BP6

Variant 1-1615612-C-A is Benign according to our data. Variant chr1-1615612-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 218832.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIB2	NM_001170687.4 linkuse as main transcript	c.-151C>A		5_prime_UTR_variant	1/20	ENST00000355826.10	NP_001164158.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIB2	ENST00000355826.10 linkuse as main transcript	c.-151C>A		5_prime_UTR_variant	1/20	1	NM_001170687.4	ENSP00000348081	P3	Q96AX9-1
	ENST00000607222.1 linkuse as main transcript	n.184G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00140

AC:

213

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000981

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.000897

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00222

AC:

405

AN:

182084

Hom.:

AF XY:

0.00234

AC XY:

234

AN XY:

99888

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00138

Gnomad ASJ exome

AF:

0.0296

Gnomad EAS exome

AF:

0.0000752

Gnomad SAS exome

AF:

0.000574

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000836

Gnomad OTH exome

AF:

0.00498

GnomAD4 exome

AF:

0.00116

AC:

1643

AN:

1417584

Hom.:

Cov.:

AF XY:

0.00117

AC XY:

824

AN XY:

702824

show subpopulations

Gnomad4 AFR exome

AF:

0.000226

Gnomad4 AMR exome

AF:

0.00129

Gnomad4 ASJ exome

AF:

0.0298

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000521

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000491

Gnomad4 OTH exome

AF:

0.00349

GnomAD4 genome

AF:

0.00139

AC:

211

AN:

152302

Hom.:

Cov.:

AF XY:

0.00142

AC XY:

106

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.0000722

Gnomad4 AMR

AF:

0.000980

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000897

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00278

Hom.:

Bravo

AF:

0.00138

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00169

AC:

ExAC

AF:

0.00113

AC:

134

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Jun 11, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.31

CADD

Benign

2.1

DANN

Uncertain

0.98

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.017

MutationTaster

Benign

1.0

A;A;A;A;N;N;N

Vest4

0.10

GERP RS

0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over