chr17-61946543-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005121.3(MED13):c.6450G>T(p.Gln2150His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,924 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_005121.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED13 | NM_005121.3 | c.6450G>T | p.Gln2150His | missense_variant | Exon 30 of 30 | ENST00000397786.7 | NP_005112.2 | |
MED13 | XM_011525551.3 | c.6291G>T | p.Gln2097His | missense_variant | Exon 29 of 29 | XP_011523853.1 | ||
MED13 | XM_011525553.4 | c.5781G>T | p.Gln1927His | missense_variant | Exon 27 of 27 | XP_011523855.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249134Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135148
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727180
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.6450G>T (p.Q2150H) alteration is located in exon 30 (coding exon 30) of the MED13 gene. This alteration results from a G to T substitution at nucleotide position 6450, causing the glutamine (Q) at amino acid position 2150 to be replaced by a histidine (H). 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