chr12-65278822-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The ENST00000355192.8(MSRB3):c.54C>T(p.Cys18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,568,746 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00048 ( 1 hom. )
Consequence
MSRB3
ENST00000355192.8 synonymous
ENST00000355192.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.96
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 Benign. Variant got -13 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 12-65278822-C-T is Benign according to our data. Variant chr12-65278822-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 227548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-65278822-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=2.96 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000427 (65/152276) while in subpopulation AMR AF= 0.000915 (14/15308). AF 95% confidence interval is 0.000552. There are 0 homozygotes in gnomad4. There are 35 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.-95C>T | 5_prime_UTR_variant | 1/7 | ENST00000308259.10 | NP_001026849.1 | ||
MSRB3 | NM_198080.4 | c.54C>T | p.Cys18= | synonymous_variant | 1/6 | NP_932346.1 | ||
MSRB3 | NM_001193460.2 | c.-259C>T | 5_prime_UTR_variant | 1/8 | NP_001180389.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSRB3 | ENST00000308259.10 | c.-95C>T | 5_prime_UTR_variant | 1/7 | 1 | NM_001031679.3 | ENSP00000312274 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 65AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000495 AC: 87AN: 175866Hom.: 0 AF XY: 0.000384 AC XY: 36AN XY: 93740
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GnomAD4 exome AF: 0.000482 AC: 683AN: 1416470Hom.: 1 Cov.: 31 AF XY: 0.000458 AC XY: 321AN XY: 700164
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GnomAD4 genome AF: 0.000427 AC: 65AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2024 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 07, 2016 | p.Cys18Cys in exon 01A of MSRB3: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. This variant has been identified in 4/12432 European chromosomes and 2/996 Latino chromosomes by the Exome Aggregation Cons ortium (ExAC, http://exac.broadinstitute.org; dbSNP rs149757878). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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