chr8-117520889-C-T
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
Consequence
NM_080651.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED30 | ENST00000297347.7 | c.13C>T | p.Pro5Ser | missense_variant | Exon 1 of 4 | 1 | NM_080651.4 | ENSP00000297347.3 | ||
MED30 | ENST00000522839.1 | c.13C>T | p.Pro5Ser | missense_variant | Exon 1 of 3 | 1 | ENSP00000431051.1 | |||
MED30 | ENST00000519879.1 | n.126C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000204 AC: 45AN: 220060Hom.: 0 AF XY: 0.000198 AC XY: 24AN XY: 121330
GnomAD4 exome AF: 0.0000607 AC: 88AN: 1448584Hom.: 0 Cov.: 31 AF XY: 0.0000681 AC XY: 49AN XY: 719354
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13C>T (p.P5S) alteration is located in exon 1 (coding exon 1) of the MED30 gene. This alteration results from a C to T substitution at nucleotide position 13, causing the proline (P) at amino acid position 5 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at