rs370198556
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_012216.4(MID2):c.2144G>A(p.Arg715Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000043 in 1,208,482 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R715W) has been classified as Uncertain significance.
Frequency
Consequence
NM_012216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.2144G>A | p.Arg715Gln | missense_variant | 10/10 | ENST00000262843.11 | |
LOC101928335 | NR_110395.1 | n.326+6021C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.2144G>A | p.Arg715Gln | missense_variant | 10/10 | 1 | NM_012216.4 | ||
ENST00000663626.2 | n.556+6021C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000144 AC: 16AN: 111411Hom.: 0 Cov.: 23 AF XY: 0.0000594 AC XY: 2AN XY: 33653
GnomAD3 exomes AF: 0.0000876 AC: 16AN: 182685Hom.: 0 AF XY: 0.0000743 AC XY: 5AN XY: 67273
GnomAD4 exome AF: 0.0000328 AC: 36AN: 1097071Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 6AN XY: 362601
GnomAD4 genome AF: 0.000144 AC: 16AN: 111411Hom.: 0 Cov.: 23 AF XY: 0.0000594 AC XY: 2AN XY: 33653
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 01, 2016 | - - |
MID2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at