chrX-107841155-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_012216.4(MID2):c.490C>G(p.Arg164Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000951 in 1,209,243 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 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. R164C) 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.490C>G | p.Arg164Gly | missense_variant | 2/10 | ENST00000262843.11 | |
MID2 | NM_001382751.1 | c.430C>G | p.Arg144Gly | missense_variant | 2/10 | ||
MID2 | NM_052817.3 | c.490C>G | p.Arg164Gly | missense_variant | 2/10 | ||
MID2 | NM_001382752.1 | c.430C>G | p.Arg144Gly | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.490C>G | p.Arg164Gly | missense_variant | 2/10 | 1 | NM_012216.4 | ||
MID2 | ENST00000443968.2 | c.490C>G | p.Arg164Gly | missense_variant | 2/10 | 1 | P1 | ||
MID2 | ENST00000451923.1 | c.430C>G | p.Arg144Gly | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000898 AC: 10AN: 111302Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33486
GnomAD3 exomes AF: 0.0000603 AC: 11AN: 182551Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67117
GnomAD4 exome AF: 0.0000956 AC: 105AN: 1097941Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 29AN XY: 363303
GnomAD4 genome ? AF: 0.0000898 AC: 10AN: 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 | Apr 18, 2023 | The c.490C>G (p.R164G) alteration is located in exon 2 (coding exon 2) of the MID2 gene. This alteration results from a C to G substitution at nucleotide position 490, causing the arginine (R) at amino acid position 164 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at