17-76469905-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001088.3(AANAT):āc.559A>Gā(p.Thr187Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,570,100 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. Variant has been reported in ClinVar as Likely benign (ā ).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.559A>G | p.Thr187Ala | missense_variant | 4/4 | ENST00000392492.8 | |
AANAT | NM_001166579.2 | c.694A>G | p.Thr232Ala | missense_variant | 7/7 | ||
AANAT | NR_110548.2 | n.815A>G | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AANAT | ENST00000392492.8 | c.559A>G | p.Thr187Ala | missense_variant | 4/4 | 1 | NM_001088.3 | P1 | |
AANAT | ENST00000250615.7 | c.694A>G | p.Thr232Ala | missense_variant | 7/7 | 1 | |||
AANAT | ENST00000587798.1 | c.*336A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000334 AC: 6AN: 179424Hom.: 0 AF XY: 0.0000310 AC XY: 3AN XY: 96698
GnomAD4 exome AF: 0.0000226 AC: 32AN: 1417948Hom.: 0 Cov.: 31 AF XY: 0.0000214 AC XY: 15AN XY: 701770
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at