chr11-86671859-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000393324.7(ME3):c.86C>A(p.Ala29Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000702 in 1,580,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.86C>A | p.Ala29Glu | missense_variant | 2/15 | ENST00000543262.6 | |
ME3 | NR_172888.1 | n.393C>A | non_coding_transcript_exon_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ME3 | ENST00000543262.6 | c.86C>A | p.Ala29Glu | missense_variant | 2/15 | 1 | NM_001161586.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000341 AC: 7AN: 205268Hom.: 0 AF XY: 0.0000349 AC XY: 4AN XY: 114450
GnomAD4 exome AF: 0.0000749 AC: 107AN: 1428710Hom.: 0 Cov.: 31 AF XY: 0.0000830 AC XY: 59AN XY: 710608
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.86C>A (p.A29E) alteration is located in exon 2 (coding exon 1) of the ME3 gene. This alteration results from a C to A substitution at nucleotide position 86, causing the alanine (A) at amino acid position 29 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