rs2276186
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_031939.6(MRO):c.489C>T(p.Ala163=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,610,724 control chromosomes in the GnomAD database, including 199,309 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 0.45 ( 16204 hom., cov: 30)
Exomes 𝑓: 0.50 ( 183105 hom. )
Consequence
MRO
NM_031939.6 synonymous
NM_031939.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.102
Genes affected
MRO (HGNC:24121): (maestro) This gene is specifically transcribed in males before and after differentiation of testis, and the encoded protein may play an important role in a mammalian sex determination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP7
?
Synonymous conserved (PhyloP=0.102 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRO | NM_031939.6 | c.489C>T | p.Ala163= | synonymous_variant | 6/8 | ENST00000398439.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRO | ENST00000398439.8 | c.489C>T | p.Ala163= | synonymous_variant | 6/8 | 1 | NM_031939.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.451 AC: 68489AN: 151696Hom.: 16200 Cov.: 30
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GnomAD3 exomes AF: 0.503 AC: 126055AN: 250404Hom.: 33070 AF XY: 0.505 AC XY: 68331AN XY: 135318
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GnomAD4 exome AF: 0.497 AC: 725629AN: 1458910Hom.: 183105 Cov.: 39 AF XY: 0.499 AC XY: 362088AN XY: 725628
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GnomAD4 genome ? AF: 0.451 AC: 68509AN: 151814Hom.: 16204 Cov.: 30 AF XY: 0.456 AC XY: 33841AN XY: 74204
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at