rs564143152
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_015335.5(MED13L):c.2012+14_2012+15del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00659 in 1,597,950 control chromosomes in the GnomAD database, including 51 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0044 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0068 ( 48 hom. )
Consequence
MED13L
NM_015335.5 intron
NM_015335.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.163
Genes affected
MED13L (HGNC:22962): (mediator complex subunit 13L) The protein encoded by this gene is a subunit of the Mediator complex, a large complex of proteins that functions as a transcriptional coactivator for most RNA polymerase II-transcribed genes. The encoded protein is involved in early development of the heart and brain. Defects in this gene are a cause of transposition of the great arteries, dextro-looped (DTGA).[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant 12-116008385-CAG-C is Benign according to our data. Variant chr12-116008385-CAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 445571.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-116008385-CAG-C is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAd4 at 3 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED13L | NM_015335.5 | c.2012+14_2012+15del | intron_variant | ENST00000281928.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED13L | ENST00000281928.9 | c.2012+14_2012+15del | intron_variant | 1 | NM_015335.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00438 AC: 666AN: 152068Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00414 AC: 1002AN: 242170Hom.: 4 AF XY: 0.00395 AC XY: 516AN XY: 130472
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GnomAD4 exome AF: 0.00682 AC: 9867AN: 1445764Hom.: 48 AF XY: 0.00661 AC XY: 4738AN XY: 717172
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GnomAD4 genome AF: 0.00438 AC: 666AN: 152186Hom.: 3 Cov.: 32 AF XY: 0.00395 AC XY: 294AN XY: 74414
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
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 | Jun 29, 2017 | - - |
Cardiac anomalies - developmental delay - facial dysmorphism syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 13, 2021 | - - |
Transposition of the great arteries, dextro-looped Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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