chr5-127339177-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001256545.2(MEGF10):c.174G>T(p.Thr58=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,612,320 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. T58T) has been classified as Benign.
Frequency
Consequence
NM_001256545.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF10 | NM_001256545.2 | c.174G>T | p.Thr58= | synonymous_variant | 3/25 | ENST00000503335.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF10 | ENST00000503335.7 | c.174G>T | p.Thr58= | synonymous_variant | 3/25 | 1 | NM_001256545.2 | P1 | |
MEGF10 | ENST00000274473.6 | c.174G>T | p.Thr58= | synonymous_variant | 4/26 | 1 | P1 | ||
MEGF10 | ENST00000418761.6 | c.174G>T | p.Thr58= | synonymous_variant | 4/15 | 1 | |||
MEGF10 | ENST00000508365.5 | c.174G>T | p.Thr58= | synonymous_variant | 3/14 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250732Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135488
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460358Hom.: 0 Cov.: 29 AF XY: 0.00000964 AC XY: 7AN XY: 726482
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.000243 AC XY: 18AN XY: 74196
ClinVar
Submissions by phenotype
MEGF10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 26, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
MEGF10-related myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at