5-127339115-T-TC
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001256545.2(MEGF10):c.117-5_117-4insC variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000507 in 1,567,582 control chromosomes in the GnomAD database, including 10 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001256545.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF10 | NM_001256545.2 | c.117-5_117-4insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000503335.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF10 | ENST00000503335.7 | c.117-5_117-4insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001256545.2 | P1 | |||
MEGF10 | ENST00000274473.6 | c.117-5_117-4insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
MEGF10 | ENST00000418761.6 | c.117-5_117-4insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
MEGF10 | ENST00000508365.5 | c.117-5_117-4insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 155AN: 152116Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00170 AC: 411AN: 241680Hom.: 6 AF XY: 0.00155 AC XY: 202AN XY: 130584
GnomAD4 exome AF: 0.000451 AC: 638AN: 1415348Hom.: 8 Cov.: 25 AF XY: 0.000425 AC XY: 300AN XY: 705060
GnomAD4 genome AF: 0.00102 AC: 156AN: 152234Hom.: 2 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74426
ClinVar
Submissions by phenotype
MEGF10-related myopathy Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at