1-1615464-C-CG
Variant names:
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
XM_047446594.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.44
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]
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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 |
---|---|---|---|---|---|---|---|---|
MIB2 | NM_001170687.4 | c.-299_-298insG | upstream_gene_variant | ENST00000355826.10 | NP_001164158.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00559 AC: 851AN: 152218Hom.: 8 Cov.: 34
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GnomAD3 exomes AF: 0.000896 AC: 101AN: 112744Hom.: 1 AF XY: 0.000833 AC XY: 52AN XY: 62432
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GnomAD4 exome AF: 0.000496 AC: 677AN: 1364332Hom.: 8 Cov.: 32 AF XY: 0.000440 AC XY: 296AN XY: 672934
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GnomAD4 genome AF: 0.00559 AC: 852AN: 152336Hom.: 8 Cov.: 34 AF XY: 0.00515 AC XY: 384AN XY: 74506
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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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at