Variant rs1388659 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0620

Variant links:

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]

MED21 links:

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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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MED21	ENST00000538186.5 linkuse as main transcript	n.225+15G>A		intron_variant, non_coding_transcript_variant		3
MED21	ENST00000544998.1 linkuse as main transcript	n.81+15G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51358

AN:

151908

Hom.:

10126

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.0325

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.336

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.375

GnomAD4 genome

AF:

0.338

AC:

51384

AN:

152026

Hom.:

10130

Cov.:

AF XY:

0.333

AC XY:

24711

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.0326

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.466

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.424

Hom.:

28659

Bravo

AF:

0.317

Asia WGS

AF:

0.144

AC:

502

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.4

DANN

Benign

0.12

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over