17-76469830-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001088.3(AANAT):c.484G>A(p.Asp162Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,452,832 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.484G>A | p.Asp162Asn | missense_variant | 4/4 | ENST00000392492.8 | |
AANAT | NM_001166579.2 | c.619G>A | p.Asp207Asn | missense_variant | 7/7 | ||
AANAT | NR_110548.2 | n.740G>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AANAT | ENST00000392492.8 | c.484G>A | p.Asp162Asn | missense_variant | 4/4 | 1 | NM_001088.3 | P1 | |
AANAT | ENST00000250615.7 | c.619G>A | p.Asp207Asn | missense_variant | 7/7 | 1 | |||
AANAT | ENST00000587798.1 | c.*261G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 3AN: 231258Hom.: 0 AF XY: 0.00000792 AC XY: 1AN XY: 126258
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1452832Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722102
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2022 | The c.484G>A (p.D162N) alteration is located in exon 4 (coding exon 3) of the AANAT gene. This alteration results from a G to A substitution at nucleotide position 484, causing the aspartic acid (D) at amino acid position 162 to be replaced by an asparagine (N). 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