18-908289-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001099733.2(ADCYAP1):c.267C>T(p.Asn89Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,612,836 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001099733.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCYAP1 | NM_001099733.2 | c.267C>T | p.Asn89Asn | synonymous_variant | Exon 4 of 5 | ENST00000450565.8 | NP_001093203.1 | |
ADCYAP1 | NM_001117.5 | c.267C>T | p.Asn89Asn | synonymous_variant | Exon 3 of 4 | NP_001108.2 | ||
ADCYAP1 | XM_005258081.5 | c.684C>T | p.Asn228Asn | synonymous_variant | Exon 5 of 6 | XP_005258138.2 | ||
ADCYAP1 | XM_047437288.1 | c.267C>T | p.Asn89Asn | synonymous_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>T | p.Asn89Asn | synonymous_variant | Exon 4 of 5 | 1 | NM_001099733.2 | ENSP00000411658.3 | ||
ADCYAP1 | ENST00000579794.1 | c.267C>T | p.Asn89Asn | synonymous_variant | Exon 3 of 4 | 1 | ENSP00000462647.1 | |||
ADCYAP1 | ENST00000269200.5 | n.265C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
ADCYAP1 | ENST00000581602.1 | n.258C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000848 AC: 129AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000743 AC: 184AN: 247500Hom.: 0 AF XY: 0.000677 AC XY: 91AN XY: 134426
GnomAD4 exome AF: 0.00126 AC: 1843AN: 1460520Hom.: 6 Cov.: 31 AF XY: 0.00118 AC XY: 854AN XY: 726556
GnomAD4 genome AF: 0.000847 AC: 129AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
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