rs201845920
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000381.4(MID1):āc.420C>Gā(p.Ser140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000802 in 1,209,532 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 28 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. S140S) has been classified as Likely benign.
Frequency
Consequence
NM_000381.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.420C>G | p.Ser140= | synonymous_variant | 2/10 | ENST00000317552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID1 | ENST00000317552.9 | c.420C>G | p.Ser140= | synonymous_variant | 2/10 | 1 | NM_000381.4 | P1 | |
ENST00000706950.1 | c.*422C>G | 3_prime_UTR_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000359 AC: 4AN: 111376Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33558
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183397Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67843
GnomAD4 exome AF: 0.0000847 AC: 93AN: 1098156Hom.: 0 Cov.: 32 AF XY: 0.0000770 AC XY: 28AN XY: 363510
GnomAD4 genome ? AF: 0.0000359 AC: 4AN: 111376Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33558
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 12, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at