rs149788020
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_030973.4(MED25):c.597C>A(p.Ala199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000794 in 1,612,612 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A199A) has been classified as Likely benign.
Frequency
Consequence
NM_030973.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED25 | NM_030973.4 | c.597C>A | p.Ala199= | synonymous_variant | 6/18 | ENST00000312865.10 | |
MED25 | NM_001378355.1 | c.597C>A | p.Ala199= | synonymous_variant | 6/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED25 | ENST00000312865.10 | c.597C>A | p.Ala199= | synonymous_variant | 6/18 | 1 | NM_030973.4 | ||
MED25 | ENST00000595185.5 | c.597C>A | p.Ala199= | synonymous_variant | 6/7 | 1 | |||
MED25 | ENST00000538643.5 | c.181-654C>A | intron_variant | 1 | |||||
MED25 | ENST00000593767.3 | c.597C>A | p.Ala199= | synonymous_variant | 6/18 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00304 AC: 463AN: 152106Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000999 AC: 244AN: 244226Hom.: 0 AF XY: 0.000834 AC XY: 111AN XY: 133110
GnomAD4 exome AF: 0.000559 AC: 816AN: 1460388Hom.: 6 Cov.: 33 AF XY: 0.000484 AC XY: 352AN XY: 726530
GnomAD4 genome ? AF: 0.00305 AC: 464AN: 152224Hom.: 2 Cov.: 32 AF XY: 0.00308 AC XY: 229AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2015 | 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
Likely benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Charcot-Marie-Tooth disease type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 30, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at