chrX-10449389-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_000381.4(MID1):āc.1983C>Gā(p.Asp661Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000893 in 111,953 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Synonymous variant affecting the same amino acid position (i.e. D661D) has been classified as Likely benign.
Frequency
Consequence
NM_000381.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.1983C>G | p.Asp661Glu | missense_variant | 10/10 | ENST00000317552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID1 | ENST00000317552.9 | c.1983C>G | p.Asp661Glu | missense_variant | 10/10 | 1 | NM_000381.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000894 AC: 1AN: 111905Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 34067
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182525Hom.: 0 AF XY: 0.0000297 AC XY: 2AN XY: 67281
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000182 AC: 2AN: 1097246Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 2AN XY: 362678
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111953Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34125
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at