1-1615464-C-CG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PVS1_StrongBP6_ModerateBS1BS2

The XM_047446594.1(MIB2):​c.10dupG​(p.Ala4GlyfsTer43) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,516,668 control chromosomes in the GnomAD database, including 16 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0056 ( 8 hom., cov: 34)
Exomes 𝑓: 0.00050 ( 8 hom. )

Consequence

MIB2
XM_047446594.1 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.997 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BP6
Variant 1-1615464-C-CG is Benign according to our data. Variant chr1-1615464-C-CG is described in ClinVar as [Benign]. Clinvar id is 791768.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00559 (852/152336) while in subpopulation AFR AF= 0.0191 (794/41592). AF 95% confidence interval is 0.018. There are 8 homozygotes in gnomad4. There are 384 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIB2NM_001170687.4 linkc.-299_-298insG upstream_gene_variant ENST00000355826.10 NP_001164158.3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIB2ENST00000355826.10 linkc.-299_-298insG upstream_gene_variant 1 NM_001170687.4 ENSP00000348081.6 Q96AX9-1E9PD12

Frequencies

GnomAD3 genomes
AF:
0.00559
AC:
851
AN:
152218
Hom.:
8
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0191
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00669
GnomAD3 exomes
AF:
0.000896
AC:
101
AN:
112744
Hom.:
1
AF XY:
0.000833
AC XY:
52
AN XY:
62432
show subpopulations
Gnomad AFR exome
AF:
0.0222
Gnomad AMR exome
AF:
0.000678
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:
0.0000237
Gnomad OTH exome
AF:
0.000282
GnomAD4 exome
AF:
0.000496
AC:
677
AN:
1364332
Hom.:
8
Cov.:
32
AF XY:
0.000440
AC XY:
296
AN XY:
672934
show subpopulations
Gnomad4 AFR exome
AF:
0.0198
Gnomad4 AMR exome
AF:
0.00107
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:
0.0000121
Gnomad4 OTH exome
AF:
0.000877
GnomAD4 genome
AF:
0.00559
AC:
852
AN:
152336
Hom.:
8
Cov.:
34
AF XY:
0.00515
AC XY:
384
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.0191
Gnomad4 AMR
AF:
0.00261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00662
Alfa
AF:
0.00248
Hom.:
0
Bravo
AF:
0.00602
Asia WGS
AF:
0.00116
AC:
4
AN:
3472

ClinVar

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

Submissions by phenotype

not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs562151581; hg19: chr1-1550844; API