Variant 1-167846372-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018417.6(ADCY10):c.2438-109G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,383,640 control chromosomes in the GnomAD database, including 87,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 7955 hom., cov: 32)

Exomes 𝑓: 0.36 ( 79389 hom. )

Consequence

ADCY10
NM_018417.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.214

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-167846372-C-A is Benign according to our data. Variant chr1-167846372-C-A is described in ClinVar as [Benign]. Clinvar id is 1183578.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY10	NM_018417.6 link	c.2438-109G>T		intron_variant		ENST00000367851.9	NP_060887.2	Q96PN6-1A0A0K0K1J8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ADCY10	ENST00000367851.9 link	c.2438-109G>T	intron_variant	1	NM_018417.6	ENSP00000356825.4	Q96PN6-1
ADCY10	ENST00000367848.1 link	c.2162-109G>T	intron_variant	1		ENSP00000356822.1	Q96PN6-2
ADCY10	ENST00000485964.5 link	n.128-109G>T	intron_variant	5		ENSP00000476402.1	V9GY51
ADCY10	ENST00000545172.5 link	c.1979-109G>T	intron_variant	2		ENSP00000441992.1	Q96PN6-4

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48277

AN:

151944

Hom.:

7951

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.320

GnomAD4 exome

AF:

0.357

AC:

439224

AN:

1231578

Hom.:

79389

AF XY:

0.353

AC XY:

219544

AN XY:

621928

show subpopulations

Gnomad4 AFR exome

AF:

0.217

Gnomad4 AMR exome

AF:

0.363

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.346

GnomAD4 genome

AF:

0.318

AC:

48289

AN:

152062

Hom.:

7955

Cov.:

AF XY:

0.315

AC XY:

23379

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.347

Gnomad4 ASJ

AF:

0.401

Gnomad4 EAS

AF:

0.433

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.325

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.341

Hom.:

4050

Bravo

AF:

0.314

Asia WGS

AF:

0.345

AC:

1199

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

-0.90

CADD

Benign

0.36

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