chr12-115984252-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_StrongBP6_Very_Strong
The NM_015335.5(MED13L):c.4459C>A(p.Pro1487Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,614,006 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1487P) has been classified as Likely benign.
Frequency
Consequence
NM_015335.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED13L | NM_015335.5 | c.4459C>A | p.Pro1487Thr | missense_variant | 20/31 | ENST00000281928.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED13L | ENST00000281928.9 | c.4459C>A | p.Pro1487Thr | missense_variant | 20/31 | 1 | NM_015335.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000156 AC: 39AN: 250800Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135518
GnomAD4 exome AF: 0.0000992 AC: 145AN: 1461740Hom.: 1 Cov.: 31 AF XY: 0.0000949 AC XY: 69AN XY: 727162
GnomAD4 genome AF: 0.000493 AC: 75AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | MED13L: BP4, BS1 - |
Likely 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 | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 11, 2020 | - - |
MED13L-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 07, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Transposition of the great arteries, dextro-looped Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at