rs61739395
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001088.3(AANAT):c.8C>A(p.Thr3Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,611,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001088.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.8C>A | p.Thr3Lys | missense_variant | Exon 2 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.143C>A | p.Thr48Lys | missense_variant | Exon 5 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.208C>A | 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.8C>A | p.Thr3Lys | missense_variant | Exon 2 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.143C>A | p.Thr48Lys | missense_variant | Exon 5 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000585649.1 | c.122C>A | p.Thr41Lys | missense_variant | Exon 1 of 3 | 1 | ENSP00000468717.1 | |||
AANAT | ENST00000587798.1 | n.8C>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000816 AC: 2AN: 244984Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133138
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1459482Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726030
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at