12-116015160-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_015335.5(MED13L):āc.1124A>Gā(p.His375Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,613,934 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_015335.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED13L | NM_015335.5 | c.1124A>G | p.His375Arg | missense_variant | 8/31 | ENST00000281928.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED13L | ENST00000281928.9 | c.1124A>G | p.His375Arg | missense_variant | 8/31 | 1 | NM_015335.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000473 AC: 119AN: 251348Hom.: 1 AF XY: 0.000618 AC XY: 84AN XY: 135848
GnomAD4 exome AF: 0.000251 AC: 367AN: 1461670Hom.: 5 Cov.: 32 AF XY: 0.000355 AC XY: 258AN XY: 727128
GnomAD4 genome AF: 0.000158 AC: 24AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2020 | - - |
Transposition of the great arteries, dextro-looped Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at