chr1-167809790-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018417.6(ADCY10):c.4721C>T(p.Thr1574Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,614,030 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 12 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 51 hom. )
Consequence
ADCY10
NM_018417.6 missense
NM_018417.6 missense
Scores
2
14
Clinical Significance
Conservation
PhyloP100: 0.460
Genes affected
ADCY10 (HGNC:21285): (adenylate cyclase 10) The protein encoded by this gene belongs to a distinct class of adenylyl cyclases that is soluble and insensitive to G protein or forskolin regulation. Activity of this protein is regulated by bicarbonate. Variation at this gene has been observed in patients with absorptive hypercalciuria. Alternatively spliced transcript variants encoding different isoforms have been observed. There is a pseudogene of this gene on chromosome 6. [provided by RefSeq, Jul 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0027578175).
BP6
?
Variant 1-167809790-G-A is Benign according to our data. Variant chr1-167809790-G-A is described in ClinVar as [Benign]. Clinvar id is 1164706.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 603 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.4721C>T | p.Thr1574Met | missense_variant | 33/33 | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.4721C>T | p.Thr1574Met | missense_variant | 33/33 | 1 | NM_018417.6 | P1 | |
ADCY10 | ENST00000367848.1 | c.4445C>T | p.Thr1482Met | missense_variant | 33/33 | 1 | |||
ADCY10 | ENST00000545172.5 | c.4262C>T | p.Thr1421Met | missense_variant | 30/30 | 2 | |||
ADCY10 | ENST00000485964.5 | c.*1657C>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00396 AC: 603AN: 152126Hom.: 12 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
603
AN:
152126
Hom.:
Cov.:
32
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: 0.00498 AC: 1252AN: 251406Hom.: 31 AF XY: 0.00455 AC XY: 618AN XY: 135882
GnomAD3 exomes
AF:
AC:
1252
AN:
251406
Hom.:
AF XY:
AC XY:
618
AN XY:
135882
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: 0.00198 AC: 2890AN: 1461786Hom.: 51 Cov.: 31 AF XY: 0.00190 AC XY: 1380AN XY: 727196
GnomAD4 exome
AF:
AC:
2890
AN:
1461786
Hom.:
Cov.:
31
AF XY:
AC XY:
1380
AN XY:
727196
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: 0.00396 AC: 603AN: 152244Hom.: 12 Cov.: 32 AF XY: 0.00617 AC XY: 459AN XY: 74450
GnomAD4 genome
?
AF:
AC:
603
AN:
152244
Hom.:
Cov.:
32
AF XY:
AC XY:
459
AN XY:
74450
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:
TwinsUK
AF:
AC:
0
ALSPAC
AF:
AC:
1
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
4
ExAC
?
AF:
AC:
431
Asia WGS
AF:
AC:
3
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 01, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.82, 0.89
.;P;P
Vest4
MVP
MPC
0.21
ClinPred
T
GERP RS
Varity_R
gMVP
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