rs2295650
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020662.4(MRS2):c.-104C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00744 in 1,101,776 control chromosomes in the GnomAD database, including 341 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 0.0096 ( 45 hom., cov: 33)
Exomes 𝑓: 0.0071 ( 296 hom. )
Consequence
MRS2
NM_020662.4 5_prime_UTR
NM_020662.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.238
Genes affected
MRS2 (HGNC:13785): (magnesium transporter MRS2) Enables magnesium ion transmembrane transporter activity. Involved in mitochondrial magnesium ion transmembrane transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRS2 | NM_020662.4 | c.-104C>G | 5_prime_UTR_variant | 1/11 | ENST00000378386.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRS2 | ENST00000378386.8 | c.-104C>G | 5_prime_UTR_variant | 1/11 | 1 | NM_020662.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00957 AC: 1456AN: 152214Hom.: 44 Cov.: 33
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GnomAD4 exome AF: 0.00710 AC: 6743AN: 949444Hom.: 296 Cov.: 12 AF XY: 0.00646 AC XY: 3090AN XY: 478034
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GnomAD4 genome ? AF: 0.00958 AC: 1459AN: 152332Hom.: 45 Cov.: 33 AF XY: 0.0117 AC XY: 869AN XY: 74490
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at