chrX-107841027-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_012216.4(MID2):c.362G>A(p.Arg121His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,209,089 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R121C) has been classified as Uncertain significance.
Frequency
Consequence
NM_012216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.362G>A | p.Arg121His | missense_variant | 2/10 | ENST00000262843.11 | |
MID2 | NM_001382751.1 | c.302G>A | p.Arg101His | missense_variant | 2/10 | ||
MID2 | NM_052817.3 | c.362G>A | p.Arg121His | missense_variant | 2/10 | ||
MID2 | NM_001382752.1 | c.302G>A | p.Arg101His | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.362G>A | p.Arg121His | missense_variant | 2/10 | 1 | NM_012216.4 | ||
MID2 | ENST00000443968.2 | c.362G>A | p.Arg121His | missense_variant | 2/10 | 1 | P1 | ||
MID2 | ENST00000451923.1 | c.302G>A | p.Arg101His | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000450 AC: 5AN: 111114Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1AN XY: 33328
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183108Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67580
GnomAD4 exome AF: 0.0000137 AC: 15AN: 1097975Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 8AN XY: 363341
GnomAD4 genome ? AF: 0.0000450 AC: 5AN: 111114Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1AN XY: 33328
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at