X-71136968-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005120.3(MED12):āc.5490A>Gā(p.Thr1830=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000257 in 1,206,231 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. T1830T) has been classified as Likely benign.
Frequency
Consequence
NM_005120.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED12 | NM_005120.3 | c.5490A>G | p.Thr1830= | synonymous_variant | 38/45 | ENST00000374080.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED12 | ENST00000374080.8 | c.5490A>G | p.Thr1830= | synonymous_variant | 38/45 | 1 | NM_005120.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000182 AC: 2AN: 109964Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32228
GnomAD3 exomes AF: 0.0000511 AC: 9AN: 176067Hom.: 0 AF XY: 0.0000799 AC XY: 5AN XY: 62615
GnomAD4 exome AF: 0.0000265 AC: 29AN: 1096267Hom.: 0 Cov.: 33 AF XY: 0.0000249 AC XY: 9AN XY: 361845
GnomAD4 genome AF: 0.0000182 AC: 2AN: 109964Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32228
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 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