rs1388659
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000538186.5(MED21):n.225+15G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,036 control chromosomes in the GnomAD database, including 10,131 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 10130 hom., cov: 32)
Exomes 𝑓: 0.30 ( 1 hom. )
Consequence
MED21
ENST00000538186.5 intron, non_coding_transcript
ENST00000538186.5 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0620
Genes affected
MED21 (HGNC:11473): (mediator complex subunit 21) This gene encodes a member of the mediator complex subunit 21 family. The encoded protein interacts with the human RNA polymerase II holoenzyme and is involved in transcriptional regulation of RNA polymerase II transcribed genes. A pseudogene of this gene is located on chromosome 8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED21 | ENST00000538186.5 | n.225+15G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
MED21 | ENST00000544998.1 | n.81+15G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.338 AC: 51358AN: 151908Hom.: 10126 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
51358
AN:
151908
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.300 AC: 3AN: 10Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 3AN XY: 10
GnomAD4 exome
AF:
AC:
3
AN:
10
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
10
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.338 AC: 51384AN: 152026Hom.: 10130 Cov.: 32 AF XY: 0.333 AC XY: 24711AN XY: 74290
GnomAD4 genome
?
AF:
AC:
51384
AN:
152026
Hom.:
Cov.:
32
AF XY:
AC XY:
24711
AN XY:
74290
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
502
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at