Variant chr11-64591802-C-T 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_144585.4(SLC22A12):c.246C>T(p.Asn82Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,612,494 control chromosomes in the GnomAD database, including 1,903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 249 hom., cov: 33)

Exomes 𝑓: 0.013 ( 1654 hom. )

Consequence

SLC22A12
NM_144585.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.0890

Variant links:

Genes affected

SLC22A12 (HGNC:17989): (solute carrier family 22 member 12) The protein encoded by this gene is a member of the organic anion transporter (OAT) family, and it acts as a urate transporter to regulate urate levels in blood. This protein is an integral membrane protein primarily found in epithelial cells of the proximal tubule of the kidney. An elevated level of serum urate, hyperuricemia, is associated with increased incidences of gout, and mutations in this gene cause renal hypouricemia type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

SLC22A12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 11-64591802-C-T is Benign according to our data. Variant chr11-64591802-C-T is described in ClinVar as [Benign]. Clinvar id is 305229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.089 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A12	NM_144585.4 link	c.246C>T	p.Asn82Asn	synonymous_variant	1/10	ENST00000377574.6	NP_653186.2	Q96S37-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A12	ENST00000377574.6 link	c.246C>T	p.Asn82Asn	synonymous_variant	1/10	1	NM_144585.4	ENSP00000366797.1		Q96S37-1

Frequencies

GnomAD3 genomes

AF:

0.0193

AC:

2931

AN:

152190

Hom.:

248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00487

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0536

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00244

Gnomad OTH

AF:

0.0162

GnomAD3 exomes

AF:

0.0374

AC:

9283

AN:

248460

Hom.:

872

AF XY:

0.0324

AC XY:

4362

AN XY:

134824

show subpopulations

Gnomad AFR exome

AF:

0.00422

Gnomad AMR exome

AF:

0.0917

Gnomad ASJ exome

AF:

0.00409

Gnomad EAS exome

AF:

0.274

Gnomad SAS exome

AF:

0.00386

Gnomad FIN exome

AF:

0.0207

Gnomad NFE exome

AF:

0.00284

Gnomad OTH exome

AF:

0.0248

GnomAD4 exome

AF:

0.0133

AC:

19459

AN:

1460186

Hom.:

1654

Cov.:

AF XY:

0.0125

AC XY:

9076

AN XY:

726510

show subpopulations

Gnomad4 AFR exome

AF:

0.00311

Gnomad4 AMR exome

AF:

0.0880

Gnomad4 ASJ exome

AF:

0.00448

Gnomad4 EAS exome

AF:

0.262

Gnomad4 SAS exome

AF:

0.00468

Gnomad4 FIN exome

AF:

0.0199

Gnomad4 NFE exome

AF:

0.00201

Gnomad4 OTH exome

AF:

0.0202

GnomAD4 genome

AF:

0.0193

AC:

2940

AN:

152308

Hom.:

249

Cov.:

AF XY:

0.0216

AC XY:

1606

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00486

Gnomad4 AMR

AF:

0.0543

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.00244

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00598

Hom.:

Bravo

AF:

0.0226

Asia WGS

AF:

0.107

AC:

370

AN:

3478

EpiCase

AF:

0.00196

EpiControl

AF:

0.00243

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
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	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 21, 2016

p.Asn82Asn in exon 1 of SLC22A12: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 26.81% (2266/8452) of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exa c.broadinstitute.org; dbSNP rs3825017). -

Dalmatian hypouricemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.8

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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