17-76468870-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001088.3(AANAT):c.124C>T(p.Pro42Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,208 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
NM_001088.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.124C>T | p.Pro42Ser | missense_variant | Exon 2 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.259C>T | p.Pro87Ser | missense_variant | Exon 5 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.324C>T | 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.124C>T | p.Pro42Ser | missense_variant | Exon 2 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.259C>T | p.Pro87Ser | missense_variant | Exon 5 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000585649.1 | c.238C>T | p.Pro80Ser | missense_variant | Exon 1 of 3 | 1 | ENSP00000468717.1 | |||
AANAT | ENST00000587798.1 | n.124C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124C>T (p.P42S) alteration is located in exon 2 (coding exon 1) of the AANAT gene. This alteration results from a C to T substitution at nucleotide position 124, causing the proline (P) at amino acid position 42 to be replaced by a serine (S). 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