16-3966932-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001116.4(ADCY9):c.2905C>T(p.Arg969Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,568 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 Uncertain significance (★).
Frequency
Consequence
NM_001116.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY9 | NM_001116.4 | c.2905C>T | p.Arg969Cys | missense_variant | 11/11 | ENST00000294016.8 | |
ADCY9 | XM_005255079.4 | c.2962C>T | p.Arg988Cys | missense_variant | 11/11 | ||
ADCY9 | XM_011522353.3 | c.2927+7737C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY9 | ENST00000294016.8 | c.2905C>T | p.Arg969Cys | missense_variant | 11/11 | 1 | NM_001116.4 | P1 | |
ADCY9 | ENST00000576936.5 | c.567+7737C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247914Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134806
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461318Hom.: 0 Cov.: 35 AF XY: 0.0000275 AC XY: 20AN XY: 726966
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.2905C>T (p.R969C) alteration is located in exon 11 (coding exon 10) of the ADCY9 gene. This alteration results from a C to T substitution at nucleotide position 2905, causing the arginine (R) at amino acid position 969 to be replaced by a cysteine (C). 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