rs11067880

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.120
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MED13LNM_015335.5 linkc.579T>C p.Asn193Asn synonymous_variant Exon 5 of 31 ENST00000281928.9 NP_056150.1 Q71F56

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MED13LENST00000281928.9 linkc.579T>C p.Asn193Asn synonymous_variant Exon 5 of 31 1 NM_015335.5 ENSP00000281928.3 Q71F56

Frequencies

GnomAD3 genomes
AF:
0.0316
AC:
4809
AN:
152220
Hom.:
241
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0128
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0205
GnomAD3 exomes
AF:
0.00823
AC:
2063
AN:
250558
Hom.:
94
AF XY:
0.00606
AC XY:
820
AN XY:
135386
show subpopulations
Gnomad AFR exome
AF:
0.110
Gnomad AMR exome
AF:
0.00612
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000229
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000291
Gnomad OTH exome
AF:
0.00344
GnomAD4 exome
AF:
0.00324
AC:
4742
AN:
1461498
Hom.:
217
Cov.:
32
AF XY:
0.00270
AC XY:
1962
AN XY:
727022
show subpopulations
Gnomad4 AFR exome
AF:
0.112
Gnomad4 AMR exome
AF:
0.00641
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000278
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000184
Gnomad4 OTH exome
AF:
0.00726
GnomAD4 genome
AF:
0.0317
AC:
4834
AN:
152338
Hom.:
245
Cov.:
32
AF XY:
0.0299
AC XY:
2225
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0128
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0203
Alfa
AF:
0.00854
Hom.:
67
Bravo
AF:
0.0358
Asia WGS
AF:
0.00779
AC:
29
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000415

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

- -

-
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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
6.5
DANN
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11067880; hg19: chr12-116460307; API