X-71118781-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_005120.3(MED12):c.27C>T(p.Tyr9Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 1,206,244 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. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005120.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000734 AC: 8AN: 109055Hom.: 0 Cov.: 20 AF XY: 0.0000958 AC XY: 3AN XY: 31319
GnomAD3 exomes AF: 0.0000569 AC: 10AN: 175607Hom.: 0 AF XY: 0.0000156 AC XY: 1AN XY: 63937
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097189Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 362771
GnomAD4 genome AF: 0.0000734 AC: 8AN: 109055Hom.: 0 Cov.: 20 AF XY: 0.0000958 AC XY: 3AN XY: 31319
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Familial thoracic aortic aneurysm and aortic dissection Benign:1
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. -
FG syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at