rs17482467

Variant names:

• chr1-167809468-A-C
• rs17482467
• NM_018417.6:c.*210T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-167809468-A-C
• chr1-167809468-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018417.6(ADCY10):​c.*210T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 583,956 control chromosomes in the GnomAD database, including 6,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.14 (1567 hom., cov: 33)
  • Exomes 𝑓: 0.14 (4749 hom.)
• Consequence: ADCY10 NM_018417.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.507
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• hypercalciuria, absorptive, 2

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• idiopathic inherited hypercalciuria

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-167809468-A-C is Benign according to our data. Variant chr1-167809468-A-C is described in ClinVar as Benign. ClinVar VariationId is 1232117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018417.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10	NM_018417.6	MANE Select	c.*210T>G		3_prime_UTR	Exon 33 of 33	NP_060887.2	Q96PN6-1
	ADCY10	NM_001297772.2		c.*210T>G		3_prime_UTR	Exon 33 of 33	NP_001284701.1	Q96PN6-2
	ADCY10	NM_001167749.3		c.*210T>G		3_prime_UTR	Exon 30 of 30	NP_001161221.1	Q96PN6-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10	ENST00000367851.9	TSL:1 MANE Select	c.*210T>G		3_prime_UTR	Exon 33 of 33	ENSP00000356825.4	Q96PN6-1
	ADCY10	ENST00000545172.5	TSL:2	c.*210T>G		3_prime_UTR	Exon 30 of 30	ENSP00000441992.1	Q96PN6-4
	ADCY10	ENST00000367848.1	TSL:1	c.*210T>G		downstream_gene	N/A	ENSP00000356822.1	Q96PN6-2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21262 AN: 152148 Hom.: 1568 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.134

GnomAD4 exome AF: 0.139 AC: 59879 AN: 431690 Hom.: 4749 Cov.: 5 AF XY: 0.143 AC XY: 32722 AN XY: 228184

African (AFR) AF: 0.150 AC: 1805 AN: 12050

American (AMR) AF: 0.0847 AC: 1431 AN: 16886

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 1411 AN: 12732

East Asian (EAS) AF: 0.0470 AC: 1326 AN: 28224

South Asian (SAS) AF: 0.224 AC: 9754 AN: 43498

European-Finnish (FIN) AF: 0.172 AC: 4408 AN: 25682

Middle Eastern (MID) AF: 0.141 AC: 258 AN: 1836

European-Non Finnish (NFE) AF: 0.136 AC: 36191 AN: 266302

Other (OTH) AF: 0.135 AC: 3295 AN: 24480

GnomAD4 genome AF: 0.140 AC: 21267 AN: 152266 Hom.: 1567 Cov.: 33 AF XY: 0.140 AC XY: 10441 AN XY: 74462

African (AFR) AF: 0.158 AC: 6548 AN: 41534

American (AMR) AF: 0.0974 AC: 1491 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3468

East Asian (EAS) AF: 0.0499 AC: 259 AN: 5192

South Asian (SAS) AF: 0.233 AC: 1126 AN: 4826

European-Finnish (FIN) AF: 0.176 AC: 1869 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9203 AN: 68016

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.136 Hom.: 557

Bravo AF: 0.132

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17482467; hg19: chr1-167778705;