11-86447145-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000393324.7(ME3):c.1300G>A(p.Glu434Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000393324.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ME3 | NM_001161586.3 | c.1300G>A | p.Glu434Lys | missense_variant | 12/15 | ENST00000543262.6 | |
ME3 | NR_172888.1 | n.1607G>A | non_coding_transcript_exon_variant | 12/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ME3 | ENST00000543262.6 | c.1300G>A | p.Glu434Lys | missense_variant | 12/15 | 1 | NM_001161586.3 | P1 | |
ME3 | ENST00000393324.7 | c.1300G>A | p.Glu434Lys | missense_variant | 11/14 | 1 | P1 | ||
ENST00000524610.1 | n.268+14503C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
ME3 | ENST00000530520.5 | n.1321G>A | non_coding_transcript_exon_variant | 11/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251170Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135752
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727240
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.1300G>A (p.E434K) alteration is located in exon 12 (coding exon 11) of the ME3 gene. This alteration results from a G to A substitution at nucleotide position 1300, causing the glutamic acid (E) at amino acid position 434 to be replaced by a lysine (K). 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