dbSNP rs74863643: MED25:p.Pro78Pro (chr19-49819225-C-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_030973.4(MED25):c.234C>G(p.Pro78Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0132 in 1,614,180 control chromosomes in the GnomAD database, including 906 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 224 hom., cov: 33)

Exomes 𝑓: 0.011 ( 682 hom. )

Consequence

MED25
NM_030973.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.85

Variant links:

Genes affected

MED25 (HGNC:28845): (mediator complex subunit 25) This gene encodes a component of the transcriptional coactivator complex termed the Mediator complex. This complex is required for transcription of most RNA polymerase II-dependent genes. The encoded protein plays a role in chromatin modification and in preinitiation complex assembly. Mutations in this gene are associated with Charcot-Marie-Tooth disease type 2B2. [provided by RefSeq, Apr 2010]

MED25 links:

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=-0.73).

BP6

Variant 19-49819225-C-G is Benign according to our data. Variant chr19-49819225-C-G is described in ClinVar as [Benign]. Clinvar id is 329878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-49819225-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.85 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MED25	NM_030973.4 link	c.234C>G	p.Pro78Pro	synonymous_variant	Exon 3 of 18	ENST00000312865.10	NP_112235.2	Q71SY5-1
MED25	NM_001378355.1 link	c.234C>G	p.Pro78Pro	synonymous_variant	Exon 3 of 18		NP_001365284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MED25	ENST00000312865.10 link	c.234C>G	p.Pro78Pro	synonymous_variant	Exon 3 of 18	1	NM_030973.4	ENSP00000326767.5		Q71SY5-1

Frequencies

GnomAD3 genomes

AF:

0.0359

AC:

5460

AN:

152230

Hom.:

223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0775

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0772

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.0279

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00156

Gnomad OTH

AF:

0.0306

GnomAD3 exomes

AF:

0.0310

AC:

7803

AN:

251418

Hom.:

424

AF XY:

0.0274

AC XY:

3718

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.0793

Gnomad AMR exome

AF:

0.0744

Gnomad ASJ exome

AF:

0.00536

Gnomad EAS exome

AF:

0.156

Gnomad SAS exome

AF:

0.0241

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.00153

Gnomad OTH exome

AF:

0.0181

GnomAD4 exome

AF:

0.0108

AC:

15822

AN:

1461832

Hom.:

682

Cov.:

AF XY:

0.0106

AC XY:

7691

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.0806

Gnomad4 AMR exome

AF:

0.0761

Gnomad4 ASJ exome

AF:

0.00417

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.0240

Gnomad4 FIN exome

AF:

0.0000749

Gnomad4 NFE exome

AF:

0.00126

Gnomad4 OTH exome

AF:

0.0210

GnomAD4 genome

AF:

0.0360

AC:

5480

AN:

152348

Hom.:

224

Cov.:

AF XY:

0.0386

AC XY:

2873

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.0777

Gnomad4 AMR

AF:

0.0775

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.0277

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00156

Gnomad4 OTH

AF:

0.0308

Alfa

AF:

0.00336

Hom.:

Bravo

AF:

0.0434

Asia WGS

AF:

0.0730

AC:

252

AN:

3478

EpiCase

AF:

0.00267

EpiControl

AF:

0.00284

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease

Benign:1

Molecular Genetics Laboratory, London Health Sciences Centre

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease type 2

Benign:1

Feb 03, 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

-0.73

CADD

Benign

1.8

DANN

Benign

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over