X-71132767-CCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT-CCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_005120.3(MED12):​c.4416-50_4416-16dupCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., 0 hem., cov: 0)
Exomes 𝑓: 0.00016 ( 1 hom. 36 hem. )
Failed GnomAD Quality Control

Consequence

MED12
NM_005120.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.294
Variant links:
Genes affected
MED12 (HGNC:11957): (mediator complex subunit 12) The initiation of transcription is controlled in part by a large protein assembly known as the preinitiation complex. A component of this preinitiation complex is a 1.2 MDa protein aggregate called Mediator. This Mediator component binds with a CDK8 subcomplex which contains the protein encoded by this gene, mediator complex subunit 12 (MED12), along with MED13, CDK8 kinase, and cyclin C. The CDK8 subcomplex modulates Mediator-polymerase II interactions and thereby regulates transcription initiation and reinitation rates. The MED12 protein is essential for activating CDK8 kinase. Defects in this gene cause X-linked Opitz-Kaveggia syndrome, also known as FG syndrome, and Lujan-Fryns syndrome. [provided by RefSeq, Aug 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000188 (17/90627) while in subpopulation EAS AF= 0.000388 (1/2580). AF 95% confidence interval is 0.000168. There are 0 homozygotes in gnomad4. There are 0 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MED12NM_005120.3 linkc.4416-50_4416-16dupCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCT intron_variant ENST00000374080.8 NP_005111.2 Q93074-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MED12ENST00000374080.8 linkc.4416-78_4416-77insCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT intron_variant 1 NM_005120.3 ENSP00000363193.3 Q93074-1

Frequencies

GnomAD3 genomes
AF:
0.000188
AC:
17
AN:
90627
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
18709
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000248
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000388
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000261
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000285
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000156
AC:
88
AN:
562789
Hom.:
1
AF XY:
0.000221
AC XY:
36
AN XY:
163151
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000324
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000429
Gnomad4 SAS exome
AF:
0.0000868
Gnomad4 FIN exome
AF:
0.000239
Gnomad4 NFE exome
AF:
0.000169
Gnomad4 OTH exome
AF:
0.000110
GnomAD4 genome
AF:
0.000188
AC:
17
AN:
90627
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
18709
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000248
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000388
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000261
Gnomad4 NFE
AF:
0.000285
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs56658066; hg19: chrX-70352617; API