NM_001088.3:c.466G>C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001088.3(AANAT):āc.466G>Cā(p.Ala156Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000117 in 1,451,584 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.466G>C | p.Ala156Pro | missense_variant | Exon 4 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.601G>C | p.Ala201Pro | missense_variant | Exon 7 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.722G>C | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AANAT | ENST00000392492.8 | c.466G>C | p.Ala156Pro | missense_variant | Exon 4 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.601G>C | p.Ala201Pro | missense_variant | Exon 7 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000587798.1 | n.*243G>C | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000468239.1 | ||||
AANAT | ENST00000587798.1 | n.*243G>C | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000875 AC: 2AN: 228618Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125110
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1451584Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 13AN XY: 721352
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466G>C (p.A156P) alteration is located in exon 4 (coding exon 3) of the AANAT gene. This alteration results from a G to C substitution at nucleotide position 466, causing the alanine (A) at amino acid position 156 to be replaced by a proline (P). 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