chr4-17614671-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_025205.5(MED28):c.17G>T(p.Gly6Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,612,532 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G6A) has been classified as Uncertain significance.
Frequency
Consequence
NM_025205.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED28 | NM_025205.5 | c.17G>T | p.Gly6Val | missense_variant | 1/4 | ENST00000237380.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED28 | ENST00000237380.12 | c.17G>T | p.Gly6Val | missense_variant | 1/4 | 1 | NM_025205.5 | P1 | |
MED28 | ENST00000503945.2 | c.8G>T | p.Gly3Val | missense_variant, NMD_transcript_variant | 1/6 | 1 | |||
MED28 | ENST00000506409.1 | n.24G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246408Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133988
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460210Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726508
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.17G>T (p.G6V) alteration is located in exon 1 (coding exon 1) of the MED28 gene. This alteration results from a G to T substitution at nucleotide position 17, causing the glycine (G) at amino acid position 6 to be replaced by a valine (V). 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