X-107841155-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_012216.4(MID2):c.490C>T(p.Arg164Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,209,243 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. 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. R164G) has been classified 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.490C>T | p.Arg164Cys | missense_variant | 2/10 | ENST00000262843.11 | |
MID2 | NM_001382751.1 | c.430C>T | p.Arg144Cys | missense_variant | 2/10 | ||
MID2 | NM_052817.3 | c.490C>T | p.Arg164Cys | missense_variant | 2/10 | ||
MID2 | NM_001382752.1 | c.430C>T | p.Arg144Cys | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.490C>T | p.Arg164Cys | missense_variant | 2/10 | 1 | NM_012216.4 | ||
MID2 | ENST00000443968.2 | c.490C>T | p.Arg164Cys | missense_variant | 2/10 | 1 | P1 | ||
MID2 | ENST00000451923.1 | c.430C>T | p.Arg144Cys | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 3AN: 111302Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33486
GnomAD3 exomes AF: 0.00000548 AC: 1AN: 182551Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67117
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097941Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363303
GnomAD4 genome ? AF: 0.0000270 AC: 3AN: 111302Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.490C>T (p.R164C) alteration is located in exon 2 (coding exon 2) of the MID2 gene. This alteration results from a C to T substitution at nucleotide position 490, causing the arginine (R) at amino acid position 164 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at