17-76468754-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001088.3(AANAT):c.8C>T(p.Thr3Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00364 in 1,611,714 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001088.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.8C>T | p.Thr3Met | missense_variant | Exon 2 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.143C>T | p.Thr48Met | missense_variant | Exon 5 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.208C>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.8C>T | p.Thr3Met | missense_variant | Exon 2 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.143C>T | p.Thr48Met | missense_variant | Exon 5 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000585649.1 | c.122C>T | p.Thr41Met | missense_variant | Exon 1 of 3 | 1 | ENSP00000468717.1 | |||
AANAT | ENST00000587798.1 | n.8C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes AF: 0.0159 AC: 2424AN: 152120Hom.: 65 Cov.: 32
GnomAD3 exomes AF: 0.00499 AC: 1222AN: 244984Hom.: 28 AF XY: 0.00392 AC XY: 522AN XY: 133138
GnomAD4 exome AF: 0.00235 AC: 3432AN: 1459476Hom.: 66 Cov.: 31 AF XY: 0.00224 AC XY: 1626AN XY: 726026
GnomAD4 genome AF: 0.0160 AC: 2436AN: 152238Hom.: 65 Cov.: 32 AF XY: 0.0154 AC XY: 1147AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at