dbSNP rs756450480: MED30:p.Pro5Thr (chr8-117520889-C-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_080651.4(MED30):c.13C>A(p.Pro5Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P5S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MED30
NM_080651.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.05

Publications

1 publications found

Variant links:

Genes affected

MED30 (HGNC:23032): (mediator complex subunit 30) The multiprotein TRAP/Mediator complex facilitates gene expression through a wide variety of transcriptional activators. MED30 is a component of this complex that appears to be metazoan specific (Baek et al., 2002 [PubMed 11909976]).[supplied by OMIM, Nov 2010]

MED30 links:

ENSG00000297933 (HGNC:):

ENSG00000297933 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080651.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MED30	NM_080651.4	MANE Select	c.13C>A	p.Pro5Thr	missense	Exon 1 of 4	NP_542382.1	Q96HR3-1
MED30	NM_001363182.2		c.13C>A	p.Pro5Thr	missense	Exon 1 of 4	NP_001350111.1
MED30	NM_001282986.2		c.13C>A	p.Pro5Thr	missense	Exon 1 of 3	NP_001269915.1	Q96HR3-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MED30	ENST00000297347.7	TSL:1 MANE Select	c.13C>A	p.Pro5Thr	missense	Exon 1 of 4	ENSP00000297347.3	Q96HR3-1
MED30	ENST00000522839.1	TSL:1	c.13C>A	p.Pro5Thr	missense	Exon 1 of 3	ENSP00000431051.1	Q96HR3-2
MED30	ENST00000920330.1		c.13C>A	p.Pro5Thr	missense	Exon 1 of 4	ENSP00000590389.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

220060

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1448584

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

719354

African (AFR)

AF:

0.00

AC:

AN:

33100

American (AMR)

AF:

0.00

AC:

AN:

43072

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25800

East Asian (EAS)

AF:

0.00

AC:

AN:

39124

South Asian (SAS)

AF:

0.00

AC:

AN:

85052

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51838

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4798

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1106120

Other (OTH)

AF:

0.00

AC:

AN:

59680

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000840

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Pathogenic

0.30

BayesDel_noAF

Pathogenic

0.20

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.051

Eigen

Uncertain

0.65

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.91

M_CAP

Benign

0.022

MetaRNN

Uncertain

0.46

MetaSVM

Benign

-0.34

MutationAssessor

Benign

1.6

PhyloP100

7.0

PrimateAI

Pathogenic

0.80

PROVEAN

Benign

-0.52

REVEL

Uncertain

0.31

Sift

Pathogenic

0.0

Sift4G

Benign

0.21

Polyphen

1.0

Vest4

0.61

MutPred

0.16

Gain of phosphorylation at S5 (P = 0.0486)

MVP

0.29

MPC

1.5

ClinPred

0.98

GERP RS

5.5

PromoterAI

0.078

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.47

gMVP

0.73

Mutation Taster

=52/48

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over