X-107840973-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_012216.4(MID2):c.308T>G(p.Ile103Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,209,712 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.308T>G | p.Ile103Ser | missense_variant | 2/10 | ENST00000262843.11 | |
MID2 | NM_001382751.1 | c.248T>G | p.Ile83Ser | missense_variant | 2/10 | ||
MID2 | NM_052817.3 | c.308T>G | p.Ile103Ser | missense_variant | 2/10 | ||
MID2 | NM_001382752.1 | c.248T>G | p.Ile83Ser | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.308T>G | p.Ile103Ser | missense_variant | 2/10 | 1 | NM_012216.4 | ||
MID2 | ENST00000443968.2 | c.308T>G | p.Ile103Ser | missense_variant | 2/10 | 1 | P1 | ||
MID2 | ENST00000451923.1 | c.248T>G | p.Ile83Ser | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000897 AC: 1AN: 111505Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33663
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1098207Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363561
GnomAD4 genome ? AF: 0.00000897 AC: 1AN: 111505Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33663
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 101 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 23, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at