rs17289102
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001114.5(ADCY7):c.2016C>T(p.Ala672=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 1,612,688 control chromosomes in the GnomAD database, including 46,036 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.18 ( 3117 hom., cov: 34)
Exomes 𝑓: 0.23 ( 42919 hom. )
Consequence
ADCY7
NM_001114.5 synonymous
NM_001114.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.14
Genes affected
ADCY7 (HGNC:238): (adenylate cyclase 7) This gene encodes a membrane-bound adenylate cyclase that catalyses the formation of cyclic AMP from ATP and is inhibitable by calcium. The product of this gene is a member of the adenylyl cyclase class-4/guanylyl cyclase enzyme family that is characterized by the presence of twelve membrane-spanning domains in its sequences. Several transcript variants have been observed for this gene, but the full-length natures of only two have been determined so far. [provided by RefSeq, Oct 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP7
?
Synonymous conserved (PhyloP=-2.14 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY7 | NM_001114.5 | c.2016C>T | p.Ala672= | synonymous_variant | 17/26 | ENST00000673801.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY7 | ENST00000673801.1 | c.2016C>T | p.Ala672= | synonymous_variant | 17/26 | NM_001114.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.179 AC: 27247AN: 152142Hom.: 3121 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
27247
AN:
152142
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.195 AC: 48738AN: 249846Hom.: 6018 AF XY: 0.204 AC XY: 27629AN XY: 135158
GnomAD3 exomes
AF:
AC:
48738
AN:
249846
Hom.:
AF XY:
AC XY:
27629
AN XY:
135158
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.233 AC: 340899AN: 1460428Hom.: 42919 Cov.: 35 AF XY: 0.234 AC XY: 169916AN XY: 726532
GnomAD4 exome
AF:
AC:
340899
AN:
1460428
Hom.:
Cov.:
35
AF XY:
AC XY:
169916
AN XY:
726532
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.179 AC: 27235AN: 152260Hom.: 3117 Cov.: 34 AF XY: 0.178 AC XY: 13238AN XY: 74454
GnomAD4 genome
?
AF:
AC:
27235
AN:
152260
Hom.:
Cov.:
34
AF XY:
AC XY:
13238
AN XY:
74454
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
249
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at