rs12679328
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_012331.5(MSRA):c.142+6215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,026 control chromosomes in the GnomAD database, including 22,049 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 0.52 ( 22049 hom., cov: 32)
Consequence
MSRA
NM_012331.5 intron
NM_012331.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.69
Genes affected
MSRA (HGNC:7377): (methionine sulfoxide reductase A) This gene encodes a ubiquitous and highly conserved protein that carries out the enzymatic reduction of methionine sulfoxide to methionine. Human and animal studies have shown the highest levels of expression in kidney and nervous tissue. The protein functions in the repair of oxidatively damaged proteins to restore biological activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSRA | NM_012331.5 | c.142+6215A>G | intron_variant | ENST00000317173.9 | |||
LOC124901885 | XR_007060815.1 | n.3031A>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRA | ENST00000317173.9 | c.142+6215A>G | intron_variant | 1 | NM_012331.5 | P1 | |||
MSRA | ENST00000441698.6 | c.142+6215A>G | intron_variant | 2 | |||||
MSRA | ENST00000518255.5 | c.142+6215A>G | intron_variant | 5 | |||||
MSRA | ENST00000521209.6 | c.-57+1774A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.516 AC: 78419AN: 151908Hom.: 22065 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: 0.516 AC: 78389AN: 152026Hom.: 22049 Cov.: 32 AF XY: 0.517 AC XY: 38448AN XY: 74312
GnomAD4 genome
?
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38448
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1603
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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