11-86449963-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000393324.7(ME3):c.1057G>C(p.Glu353Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,112 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ME3 | NM_001161586.3 | c.1057G>C | p.Glu353Gln | missense_variant | 10/15 | ENST00000543262.6 | |
ME3 | NR_172888.1 | n.1364G>C | non_coding_transcript_exon_variant | 10/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ME3 | ENST00000543262.6 | c.1057G>C | p.Glu353Gln | missense_variant | 10/15 | 1 | NM_001161586.3 | P1 | |
ENST00000524610.1 | n.268+17321C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251354Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135836
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461794Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727180
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.1057G>C (p.E353Q) alteration is located in exon 10 (coding exon 9) of the ME3 gene. This alteration results from a G to C substitution at nucleotide position 1057, causing the glutamic acid (E) at amino acid position 353 to be replaced by a glutamine (Q). 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