X-71121319-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005120.3(MED12):c.736-8A>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 1,204,692 control chromosomes in the GnomAD database, including 36,280 homozygotes. There are 109,353 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005120.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED12 | NM_005120.3 | c.736-8A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000374080.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED12 | ENST00000374080.8 | c.736-8A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005120.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.222 AC: 24609AN: 110724Hom.: 2629 Cov.: 23 AF XY: 0.210 AC XY: 6906AN XY: 32956
GnomAD3 exomes AF: 0.225 AC: 40789AN: 181546Hom.: 3776 AF XY: 0.231 AC XY: 15567AN XY: 67404
GnomAD4 exome AF: 0.288 AC: 315087AN: 1093912Hom.: 33653 Cov.: 31 AF XY: 0.285 AC XY: 102437AN XY: 359640
GnomAD4 genome AF: 0.222 AC: 24608AN: 110780Hom.: 2627 Cov.: 23 AF XY: 0.209 AC XY: 6916AN XY: 33022
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 14, 2014 | - - |
X-linked intellectual disability with marfanoid habitus Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
FG syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
FG syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Blepharophimosis - intellectual disability syndrome, MKB type Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at