rs11067880
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015335.5(MED13L):c.579T>C(p.Asn193Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,613,836 control chromosomes in the GnomAD database, including 462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.032 ( 245 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 217 hom. )
Consequence
MED13L
NM_015335.5 synonymous
NM_015335.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.120
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 12-116022502-A-G is Benign according to our data. Variant chr12-116022502-A-G is described in ClinVar as [Benign]. Clinvar id is 415972.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-116022502-A-G is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.12 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0316 AC: 4809AN: 152220Hom.: 241 Cov.: 32
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GnomAD3 exomes AF: 0.00823 AC: 2063AN: 250558Hom.: 94 AF XY: 0.00606 AC XY: 820AN XY: 135386
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GnomAD4 exome AF: 0.00324 AC: 4742AN: 1461498Hom.: 217 Cov.: 32 AF XY: 0.00270 AC XY: 1962AN XY: 727022
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GnomAD4 genome AF: 0.0317 AC: 4834AN: 152338Hom.: 245 Cov.: 32 AF XY: 0.0299 AC XY: 2225AN XY: 74506
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Nov 05, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Transposition of the great arteries, dextro-looped Benign:1
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at