22-20537211-C-CCCTA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000263205.11(MED15):c.154_155insCCTA(p.Arg52fs) variant causes a frameshift, stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0717 in 1,611,884 control chromosomes in the GnomAD database, including 7,814 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.060 ( 648 hom., cov: 33)
Exomes 𝑓: 0.073 ( 7166 hom. )
Consequence
MED15
ENST00000263205.11 frameshift, stop_gained, splice_region
ENST00000263205.11 frameshift, stop_gained, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.147
Genes affected
MED15 (HGNC:14248): (mediator complex subunit 15) The protein encoded by this gene is a subunit of the multiprotein complexes PC2 and ARC/DRIP and may function as a transcriptional coactivator in RNA polymerase II transcription. This gene contains stretches of trinucleotide repeats and is located in the chromosome 22 region which is deleted in DiGeorge syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 22-20537211-C-CCCTA is Benign according to our data. Variant chr22-20537211-C-CCCTA is described in ClinVar as [Benign]. Clinvar id is 770675.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0604 AC: 9190AN: 152166Hom.: 648 Cov.: 33
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GnomAD3 exomes AF: 0.0934 AC: 23446AN: 250970Hom.: 2146 AF XY: 0.0972 AC XY: 13189AN XY: 135640
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GnomAD4 exome AF: 0.0728 AC: 106319AN: 1459602Hom.: 7166 Cov.: 30 AF XY: 0.0762 AC XY: 55351AN XY: 726268
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GnomAD4 genome AF: 0.0604 AC: 9191AN: 152282Hom.: 648 Cov.: 33 AF XY: 0.0642 AC XY: 4777AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 12, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at