8-117520889-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080651.4(MED30):c.13C>T(p.Pro5Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000587 in 1,600,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000061 ( 0 hom. )
Consequence
MED30
NM_080651.4 missense
NM_080651.4 missense
Scores
3
5
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.05
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.016767174).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED30 | NM_080651.4 | c.13C>T | p.Pro5Ser | missense_variant | 1/4 | ENST00000297347.7 | |
MED30 | NM_001363182.2 | c.13C>T | p.Pro5Ser | missense_variant | 1/4 | ||
MED30 | NM_001282986.2 | c.13C>T | p.Pro5Ser | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED30 | ENST00000297347.7 | c.13C>T | p.Pro5Ser | missense_variant | 1/4 | 1 | NM_080651.4 | P1 | |
MED30 | ENST00000522839.1 | c.13C>T | p.Pro5Ser | missense_variant | 1/3 | 1 | |||
MED30 | ENST00000519879.1 | n.126C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000204 AC: 45AN: 220060Hom.: 0 AF XY: 0.000198 AC XY: 24AN XY: 121330
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GnomAD4 exome AF: 0.0000607 AC: 88AN: 1448584Hom.: 0 Cov.: 31 AF XY: 0.0000681 AC XY: 49AN XY: 719354
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at