6-131621865-G-GA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004830.4(MED23):c.495+15_495+16insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 1,569,622 control chromosomes in the GnomAD database, including 79 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 40 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 39 hom. )
Consequence
MED23
NM_004830.4 intron
NM_004830.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.403
Genes affected
MED23 (HGNC:2372): (mediator complex subunit 23) The activation of gene transcription is a multistep process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators to direct transcriptional initiation by the RNA polymerase II apparatus. The protein encoded by this gene is a subunit of the CRSP (cofactor required for SP1 activation) complex, which, along with TFIID, is required for efficient activation by SP1. This protein is also a component of other multisubunit complexes e.g. thyroid hormone receptor-(TR-) associated proteins which interact with TR and facilitate TR function on DNA templates in conjunction with initiation factors and cofactors. This protein also acts as a metastasis suppressor. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 6-131621865-G-GA is Benign according to our data. Variant chr6-131621865-G-GA is described in ClinVar as [Likely_benign]. Clinvar id is 445425.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0131 (1986/152184) while in subpopulation AFR AF= 0.0427 (1775/41522). AF 95% confidence interval is 0.0411. There are 40 homozygotes in gnomad4. There are 906 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 40 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED23 | NM_004830.4 | c.495+15_495+16insT | intron_variant | ENST00000368068.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED23 | ENST00000368068.8 | c.495+15_495+16insT | intron_variant | 1 | NM_004830.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0131 AC: 1987AN: 152068Hom.: 40 Cov.: 32
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GnomAD3 exomes AF: 0.00331 AC: 790AN: 238662Hom.: 17 AF XY: 0.00238 AC XY: 307AN XY: 129212
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GnomAD4 exome AF: 0.00130 AC: 1841AN: 1417438Hom.: 39 Cov.: 25 AF XY: 0.00111 AC XY: 782AN XY: 705902
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GnomAD4 genome ? AF: 0.0131 AC: 1986AN: 152184Hom.: 40 Cov.: 32 AF XY: 0.0122 AC XY: 906AN XY: 74404
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 15, 2017 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at