19-16576311-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004831.5(MED26):c.1519G>T(p.Ala507Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,112 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004831.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED26 | NM_004831.5 | c.1519G>T | p.Ala507Ser | missense_variant | Exon 3 of 3 | ENST00000263390.8 | NP_004822.2 | |
LOC105372295 | XR_936359.3 | n.475-1855C>A | intron_variant | Intron 1 of 2 | ||||
LOC105372295 | XR_936360.3 | n.260-1855C>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED26 | ENST00000263390.8 | c.1519G>T | p.Ala507Ser | missense_variant | Exon 3 of 3 | 1 | NM_004831.5 | ENSP00000263390.3 | ||
MED26 | ENST00000611692 | c.*884G>T | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000484490.1 | ||||
ENSG00000141979 | ENST00000409035.1 | n.1211+332G>T | intron_variant | Intron 4 of 11 | 2 | ENSP00000386951.2 | ||||
MED26 | ENST00000597244.1 | n.2467G>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250828Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135644
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460950Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726798
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1519G>T (p.A507S) alteration is located in exon 3 (coding exon 3) of the MED26 gene. This alteration results from a G to T substitution at nucleotide position 1519, causing the alanine (A) at amino acid position 507 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