chr3-123284618-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS1
The NM_183357.3(ADCY5):c.3776C>T(p.Pro1259Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000873 in 1,614,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1259P) has been classified as Likely benign.
Frequency
Consequence
NM_183357.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY5 | NM_183357.3 | c.3776C>T | p.Pro1259Leu | missense_variant | 21/21 | ENST00000462833.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY5 | ENST00000462833.6 | c.3776C>T | p.Pro1259Leu | missense_variant | 21/21 | 1 | NM_183357.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251414Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135876
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.0000825 AC XY: 60AN XY: 727234
GnomAD4 genome AF: 0.000118 AC: 18AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
ADCY5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at