rs10784460
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_120431.1(MSRB3-AS1):n.550-2670C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,006 control chromosomes in the GnomAD database, including 11,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 11002 hom., cov: 32)
Consequence
MSRB3-AS1
NR_120431.1 intron, non_coding_transcript
NR_120431.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.56
Genes affected
MSRB3-AS1 (HGNC:53386): (MSRB3 antisense RNA 1)
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3-AS1 | NR_120431.1 | n.550-2670C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSRB3-AS1 | ENST00000537250.5 | n.376-2670C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
MSRB3 | ENST00000446731.2 | c.265+15979G>A | intron_variant | 3 | ENSP00000404903 | |||||
MSRB3 | ENST00000541189.5 | c.436+15979G>A | intron_variant | 3 | ENSP00000440722 | |||||
MSRB3 | ENST00000647481.1 | c.195+15979G>A | intron_variant | ENSP00000496162 |
Frequencies
GnomAD3 genomes AF: 0.368 AC: 55919AN: 151890Hom.: 10997 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.368 AC: 55936AN: 152006Hom.: 11002 Cov.: 32 AF XY: 0.367 AC XY: 27243AN XY: 74290
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1239
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at