Variant rs3213588 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.*72C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 1,538,322 control chromosomes in the GnomAD database, including 140,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 20867 hom., cov: 32)

Exomes 𝑓: 0.41 ( 119857 hom. )

Consequence

ADCY10
NM_018417.6 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0450

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=-0.86).

BP6

Variant 1-167809606-G-A is Benign according to our data. Variant chr1-167809606-G-A is described in ClinVar as [Benign]. Clinvar id is 1250999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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.*72C>T		3_prime_UTR_variant	33/33	ENST00000367851.9	NP_060887.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY10	ENST00000367851.9 linkuse as main transcript	c.*72C>T	3_prime_UTR_variant	33/33	1	NM_018417.6	ENSP00000356825	P1	Q96PN6-1
ADCY10	ENST00000545172.5 linkuse as main transcript	c.*72C>T	3_prime_UTR_variant	30/30	2		ENSP00000441992		Q96PN6-4
ADCY10	ENST00000485964.5 linkuse as main transcript		downstream_gene_variant		5		ENSP00000476402

Frequencies

GnomAD3 genomes

AF:

0.496

AC:

75438

AN:

151976

Hom.:

20824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.756

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.483

GnomAD4 exome

AF:

0.408

AC:

566029

AN:

1386228

Hom.:

119857

Cov.:

AF XY:

0.407

AC XY:

282317

AN XY:

694168

show subpopulations

Gnomad4 AFR exome

AF:

0.763

Gnomad4 AMR exome

AF:

0.331

Gnomad4 ASJ exome

AF:

0.469

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.374

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.409

Gnomad4 OTH exome

AF:

0.423

GnomAD4 genome

AF:

0.497

AC:

75533

AN:

152094

Hom.:

20867

Cov.:

AF XY:

0.492

AC XY:

36555

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.401

Gnomad4 ASJ

AF:

0.483

Gnomad4 EAS

AF:

0.173

Gnomad4 SAS

AF:

0.371

Gnomad4 FIN

AF:

0.429

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.421

Hom.:

28915

Bravo

AF:

0.506

Asia WGS

AF:

0.314

AC:

1094

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

-0.86

CADD

Benign

1.7

DANN

Benign

0.39

Splicing

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