NM_004990.4:c.873C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004990.4(MARS1):c.873C>T(p.Ala291Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,614,024 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004990.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MARS1 | NM_004990.4 | c.873C>T | p.Ala291Ala | synonymous_variant | Exon 8 of 21 | ENST00000262027.10 | NP_004981.2 | |
MARS1 | XM_047428851.1 | c.171C>T | p.Ala57Ala | synonymous_variant | Exon 4 of 17 | XP_047284807.1 | ||
MARS1 | XM_047428852.1 | c.873C>T | p.Ala291Ala | synonymous_variant | Exon 8 of 15 | XP_047284808.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00550 AC: 837AN: 152114Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00130 AC: 327AN: 251458Hom.: 4 AF XY: 0.000986 AC XY: 134AN XY: 135904
GnomAD4 exome AF: 0.000562 AC: 821AN: 1461792Hom.: 6 Cov.: 31 AF XY: 0.000481 AC XY: 350AN XY: 727190
GnomAD4 genome AF: 0.00555 AC: 845AN: 152232Hom.: 9 Cov.: 32 AF XY: 0.00547 AC XY: 407AN XY: 74426
ClinVar
Submissions by phenotype
not specified Benign:2
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Charcot-Marie-Tooth disease Benign:1
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Charcot-Marie-Tooth disease axonal type 2U;C4225400:Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at