X-40659464-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004229.4(MED14):c.3828T>A(p.Asp1276Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,209,844 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004229.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED14 | ENST00000324817.6 | c.3828T>A | p.Asp1276Glu | missense_variant | Exon 27 of 31 | 1 | NM_004229.4 | ENSP00000323720.1 | ||
MED14 | ENST00000433003.1 | c.525T>A | p.Asp175Glu | missense_variant | Exon 3 of 6 | 1 | ENSP00000411357.1 | |||
MED14 | ENST00000472736.1 | n.356T>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 5 | |||||
MED14 | ENST00000416199.5 | c.-130T>A | upstream_gene_variant | 2 | ENSP00000392586.1 |
Frequencies
GnomAD3 genomes AF: 0.000408 AC: 46AN: 112608Hom.: 0 Cov.: 23 AF XY: 0.000403 AC XY: 14AN XY: 34750
GnomAD3 exomes AF: 0.000116 AC: 21AN: 180914Hom.: 0 AF XY: 0.0000611 AC XY: 4AN XY: 65496
GnomAD4 exome AF: 0.0000510 AC: 56AN: 1097181Hom.: 0 Cov.: 29 AF XY: 0.0000414 AC XY: 15AN XY: 362619
GnomAD4 genome AF: 0.000408 AC: 46AN: 112663Hom.: 0 Cov.: 23 AF XY: 0.000402 AC XY: 14AN XY: 34815
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3828T>A (p.D1276E) alteration is located in exon 27 (coding exon 27) of the MED14 gene. This alteration results from a T to A substitution at nucleotide position 3828, causing the aspartic acid (D) at amino acid position 1276 to be replaced by a glutamic acid (E). 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