rs149799520
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001099733.2(ADCYAP1):c.267C>A(p.Asn89Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N89N) has been classified as Likely benign.
Frequency
Consequence
NM_001099733.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCYAP1 | NM_001099733.2 | c.267C>A | p.Asn89Lys | missense_variant | Exon 4 of 5 | ENST00000450565.8 | NP_001093203.1 | |
ADCYAP1 | NM_001117.5 | c.267C>A | p.Asn89Lys | missense_variant | Exon 3 of 4 | NP_001108.2 | ||
ADCYAP1 | XM_005258081.5 | c.684C>A | p.Asn228Lys | missense_variant | Exon 5 of 6 | XP_005258138.2 | ||
ADCYAP1 | XM_047437288.1 | c.267C>A | p.Asn89Lys | missense_variant | Exon 4 of 5 | XP_047293244.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADCYAP1 | ENST00000450565.8 | c.267C>A | p.Asn89Lys | missense_variant | Exon 4 of 5 | 1 | NM_001099733.2 | ENSP00000411658.3 | ||
ADCYAP1 | ENST00000579794.1 | c.267C>A | p.Asn89Lys | missense_variant | Exon 3 of 4 | 1 | ENSP00000462647.1 | |||
ADCYAP1 | ENST00000269200.5 | n.265C>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
ADCYAP1 | ENST00000581602.1 | n.258C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460524Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726558
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.267C>A (p.N89K) alteration is located in exon 4 (coding exon 3) of the ADCYAP1 gene. This alteration results from a C to A substitution at nucleotide position 267, causing the asparagine (N) at amino acid position 89 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.