chr3-151156270-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001393769.1(MED12L):c.666G>T(p.Glu222Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,613,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001393769.1 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 |
---|---|---|---|---|---|---|---|
MED12L | NM_001393769.1 | c.666G>T | p.Glu222Asp | missense_variant | 6/45 | ENST00000687756.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED12L | ENST00000687756.1 | c.666G>T | p.Glu222Asp | missense_variant | 6/45 | NM_001393769.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000288 AC: 72AN: 249788Hom.: 0 AF XY: 0.000348 AC XY: 47AN XY: 134978
GnomAD4 exome AF: 0.000222 AC: 325AN: 1460816Hom.: 0 Cov.: 30 AF XY: 0.000261 AC XY: 190AN XY: 726654
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74376
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 21, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at