rs17667932
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080651.4(MED30):c.442-2746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 152,328 control chromosomes in the GnomAD database, including 508 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 0.075 ( 508 hom., cov: 33)
Consequence
MED30
NM_080651.4 intron
NM_080651.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.997
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED30 | NM_080651.4 | c.442-2746T>C | intron_variant | ENST00000297347.7 | |||
MED30 | NM_001363182.2 | c.*1004T>C | 3_prime_UTR_variant | 4/4 | |||
MED30 | NM_001282986.2 | c.337-2746T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED30 | ENST00000297347.7 | c.442-2746T>C | intron_variant | 1 | NM_080651.4 | P1 | |||
MED30 | ENST00000522839.1 | c.337-2746T>C | intron_variant | 1 | |||||
MED30 | ENST00000519391.1 | n.465-2746T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0752 AC: 11453AN: 152210Hom.: 508 Cov.: 33
GnomAD3 genomes
?
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11453
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152210
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0753 AC: 11463AN: 152328Hom.: 508 Cov.: 33 AF XY: 0.0782 AC XY: 5821AN XY: 74480
GnomAD4 genome
?
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AC:
11463
AN:
152328
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33
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5821
AN XY:
74480
Gnomad4 AFR
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Asia WGS
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310
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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