rs764789036
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2
The NM_005120.3(MED12):c.6315_6320delACAGCA(p.Gln2106_Gln2107del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,159,273 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 58 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005120.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000202 AC: 22AN: 108870Hom.: 0 Cov.: 23 AF XY: 0.000190 AC XY: 6AN XY: 31608
GnomAD3 exomes AF: 0.000106 AC: 12AN: 113583Hom.: 0 AF XY: 0.0000738 AC XY: 3AN XY: 40659
GnomAD4 exome AF: 0.000158 AC: 166AN: 1050403Hom.: 0 AF XY: 0.000152 AC XY: 52AN XY: 341557
GnomAD4 genome AF: 0.000202 AC: 22AN: 108870Hom.: 0 Cov.: 23 AF XY: 0.000190 AC XY: 6AN XY: 31608
ClinVar
Submissions by phenotype
not provided Benign:2
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MED12: BS2 -
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