12-65278794-GC-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 6P and 5B. PVS1_StrongPM2BP6BS1
The NM_198080.4(MSRB3):c.31delC(p.Leu11SerfsTer40) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,571,156 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00064 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000063 ( 0 hom. )
Consequence
MSRB3
NM_198080.4 frameshift
NM_198080.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.30
Genes affected
MSRB3 (HGNC:27375): (methionine sulfoxide reductase B3) The protein encoded by this gene catalyzes the reduction of methionine sulfoxide to methionine. This enzyme acts as a monomer and requires zinc as a cofactor. Several transcript variants encoding two different isoforms have been found for this gene. One of the isoforms localizes to mitochondria while the other localizes to endoplasmic reticula. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 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 0.946 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-65278794-GC-G is Benign according to our data. Variant chr12-65278794-GC-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 432258.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=2}.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000637 (97/152208) while in subpopulation AFR AF= 0.00229 (95/41542). AF 95% confidence interval is 0.00192. There are 0 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.-118delC | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000308259.10 | NP_001026849.1 | ||
MSRB3 | NM_198080.4 | c.31delC | p.Leu11SerfsTer40 | frameshift_variant | Exon 1 of 6 | NP_932346.1 | ||
MSRB3 | NM_001193460.2 | c.-282delC | 5_prime_UTR_variant | Exon 1 of 8 | NP_001180389.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000638 AC: 97AN: 152090Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000151 AC: 27AN: 178768Hom.: 0 AF XY: 0.0000836 AC XY: 8AN XY: 95712
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GnomAD4 exome AF: 0.0000634 AC: 90AN: 1418948Hom.: 0 Cov.: 31 AF XY: 0.0000499 AC XY: 35AN XY: 701790
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GnomAD4 genome AF: 0.000637 AC: 97AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000685 AC XY: 51AN XY: 74412
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 31, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 2017 | The c.31delC variant in the MSRB3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.31delC variant causes a frameshift starting with codon Leucine 11, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 40 of the new reading frame, denoted p.Leu11SerfsX40. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.31delC variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.31delC as a variant of uncertain significance. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 04, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at