2-218269498-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000248450.9(AAMP):āc.158A>Gā(p.Glu53Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000641 in 1,614,172 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 (ā ).
Frequency
Consequence
ENST00000248450.9 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AAMP | NM_001087.5 | c.158A>G | p.Glu53Gly | missense_variant | 2/11 | ENST00000248450.9 | NP_001078.2 | |
AAMP | NM_001302545.2 | c.161A>G | p.Glu54Gly | missense_variant | 2/11 | NP_001289474.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AAMP | ENST00000248450.9 | c.158A>G | p.Glu53Gly | missense_variant | 2/11 | 1 | NM_001087.5 | ENSP00000248450 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000398 AC: 100AN: 251474Hom.: 1 AF XY: 0.000434 AC XY: 59AN XY: 135920
GnomAD4 exome AF: 0.000668 AC: 976AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.000652 AC XY: 474AN XY: 727246
GnomAD4 genome AF: 0.000387 AC: 59AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.158A>G (p.E53G) alteration is located in exon 2 (coding exon 2) of the AAMP gene. This alteration results from a A to G substitution at nucleotide position 158, causing the glutamic acid (E) at amino acid position 53 to be replaced by a glycine (G). 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