17-76468900-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001088.3(AANAT):āc.154G>Cā(p.Glu52Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,460,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001088.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.154G>C | p.Glu52Gln | missense_variant | Exon 2 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.289G>C | p.Glu97Gln | missense_variant | Exon 5 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.354G>C | non_coding_transcript_exon_variant | Exon 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AANAT | ENST00000392492.8 | c.154G>C | p.Glu52Gln | missense_variant | Exon 2 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.289G>C | p.Glu97Gln | missense_variant | Exon 5 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000585649.1 | c.268G>C | p.Glu90Gln | missense_variant | Exon 1 of 3 | 1 | ENSP00000468717.1 | |||
AANAT | ENST00000587798.1 | n.154G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134890
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460808Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726694
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154G>C (p.E52Q) alteration is located in exon 2 (coding exon 1) of the AANAT gene. This alteration results from a G to C substitution at nucleotide position 154, causing the glutamic acid (E) at amino acid position 52 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