rs765698306
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_000381.4(MID1):c.342C>T(p.Ala114=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,209,538 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000381.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.342C>T | p.Ala114= | synonymous_variant | 2/10 | ENST00000317552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID1 | ENST00000317552.9 | c.342C>T | p.Ala114= | synonymous_variant | 2/10 | 1 | NM_000381.4 | P1 | |
ENST00000706950.1 | c.*344C>T | 3_prime_UTR_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000539 AC: 6AN: 111414Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33592
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183347Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67797
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1098072Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 7AN XY: 363426
GnomAD4 genome ? AF: 0.0000538 AC: 6AN: 111466Hom.: 0 Cov.: 22 AF XY: 0.0000594 AC XY: 2AN XY: 33654
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | MID1: BP4, BP7, BS2 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 28, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at