rs1555905154
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_000381.4(MID1):c.567C>T(p.Thr189Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,209,781 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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). Synonymous variant affecting the same amino acid position (i.e. T189T) has been classified as Likely benign.
Frequency
Consequence
NM_000381.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.567C>T | p.Thr189Thr | synonymous_variant | Exon 2 of 10 | ENST00000317552.9 | NP_000372.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MID1 | ENST00000317552.9 | c.567C>T | p.Thr189Thr | synonymous_variant | Exon 2 of 10 | 1 | NM_000381.4 | ENSP00000312678.4 | ||
MID1 | ENST00000380782.6 | c.567C>T | p.Thr189Thr | synonymous_variant | Exon 2 of 10 | 1 | ENSP00000370159.1 | |||
ENSG00000291314 | ENST00000706950.1 | c.*569C>T | 3_prime_UTR_variant | Exon 2 of 2 | ENSP00000516670.1 |
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111637Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33823
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1098144Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363498
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111637Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33823
ClinVar
Submissions by phenotype
not specified Uncertain:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at