chrX-71118708-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005120.3(MED12):c.-47A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000907 in 1,135,790 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005120.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED12 | ENST00000374080 | c.-47A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 45 | 1 | NM_005120.3 | ENSP00000363193.3 | |||
MED12 | ENST00000374080 | c.-47A>T | 5_prime_UTR_variant | Exon 1 of 45 | 1 | NM_005120.3 | ENSP00000363193.3 |
Frequencies
GnomAD3 genomes AF: 0.000103 AC: 11AN: 106941Hom.: 0 Cov.: 20 AF XY: 0.0000658 AC XY: 2AN XY: 30409
GnomAD3 exomes AF: 0.000140 AC: 19AN: 135357Hom.: 0 AF XY: 0.000213 AC XY: 9AN XY: 42311
GnomAD4 exome AF: 0.0000894 AC: 92AN: 1028849Hom.: 0 Cov.: 23 AF XY: 0.000109 AC XY: 34AN XY: 312445
GnomAD4 genome AF: 0.000103 AC: 11AN: 106941Hom.: 0 Cov.: 20 AF XY: 0.0000658 AC XY: 2AN XY: 30409
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at