X-10501436-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001193278.1(MID1):c.880G>A(p.Glu294Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,153,689 control chromosomes in the GnomAD database, including 80 homozygotes. There are 4,381 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001193278.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.757-5745G>A | intron_variant | ENST00000317552.9 | NP_000372.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MID1 | ENST00000317552.9 | c.757-5745G>A | intron_variant | 1 | NM_000381.4 | ENSP00000312678.4 | ||||
MID1 | ENST00000380782.6 | c.757-5745G>A | intron_variant | 1 | ENSP00000370159.1 |
Frequencies
GnomAD3 genomes AF: 0.00758 AC: 846AN: 111607Hom.: 4 Cov.: 23 AF XY: 0.00663 AC XY: 224AN XY: 33767
GnomAD3 exomes AF: 0.00659 AC: 645AN: 97874Hom.: 4 AF XY: 0.00670 AC XY: 245AN XY: 36568
GnomAD4 exome AF: 0.0127 AC: 13273AN: 1042029Hom.: 76 Cov.: 29 AF XY: 0.0122 AC XY: 4158AN XY: 341091
GnomAD4 genome AF: 0.00757 AC: 845AN: 111660Hom.: 4 Cov.: 23 AF XY: 0.00659 AC XY: 223AN XY: 33830
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at