Variant 1-167856368-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_018417.6(ADCY10):c.1968T>C(p.Phe656Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,613,870 control chromosomes in the GnomAD database, including 18,648 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1955 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16693 hom. )

Consequence

ADCY10
NM_018417.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.00700

Variant links:

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]

ADCY10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 1-167856368-A-G is Benign according to our data. Variant chr1-167856368-A-G is described in ClinVar as [Benign]. Clinvar id is 1164409.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.007 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY10	NM_018417.6 linkuse as main transcript	c.1968T>C	p.Phe656Phe	synonymous_variant	17/33	ENST00000367851.9	NP_060887.2	Q96PN6-1A0A0K0K1J8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADCY10	ENST00000367851.9 linkuse as main transcript	c.1968T>C	p.Phe656Phe	synonymous_variant	17/33	1	NM_018417.6	ENSP00000356825.4	Q96PN6-1
ADCY10	ENST00000367848.1 linkuse as main transcript	c.1692T>C	p.Phe564Phe	synonymous_variant	17/33	1		ENSP00000356822.1	Q96PN6-2
ADCY10	ENST00000545172.5 linkuse as main transcript	c.1509T>C	p.Phe503Phe	synonymous_variant	14/30	2		ENSP00000441992.1	Q96PN6-4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

21977

AN:

151988

Hom.:

1944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0972

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.188

AC:

47201

AN:

251390

Hom.:

5893

AF XY:

0.181

AC XY:

24622

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.0946

Gnomad AMR exome

AF:

0.333

Gnomad ASJ exome

AF:

0.151

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.189

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.135

AC:

197580

AN:

1461764

Hom.:

16693

Cov.:

AF XY:

0.137

AC XY:

99276

AN XY:

727176

show subpopulations

Gnomad4 AFR exome

AF:

0.0983

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.150

Gnomad4 EAS exome

AF:

0.416

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.146

GnomAD4 genome

AF:

0.145

AC:

22010

AN:

152106

Hom.:

1955

Cov.:

AF XY:

0.154

AC XY:

11421

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0974

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.131

Hom.:

2443

Bravo

AF:

0.150

Asia WGS

AF:

0.312

AC:

1085

AN:

3478

EpiCase

AF:

0.123

EpiControl

AF:

0.123

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.6

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over