Genetic Variant SLC22A12:p.Leu437Leu (chr11-64600390-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

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

The NM_144585.4(SLC22A12):c.1309T>C(p.Leu437Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,605,460 control chromosomes in the GnomAD database, including 49,700 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 10860 hom., cov: 33)

Exomes 𝑓: 0.22 ( 38840 hom. )

Consequence

SLC22A12
NM_144585.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.441

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:

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=-0.71).

BP6

Variant 11-64600390-T-C is Benign according to our data. Variant chr11-64600390-T-C is described in ClinVar as [Benign]. Clinvar id is 305244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.441 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A12	NM_144585.4 link	c.1309T>C	p.Leu437Leu	synonymous_variant	Exon 8 of 10	ENST00000377574.6	NP_653186.2	Q96S37-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A12	ENST00000377574.6 link	c.1309T>C	p.Leu437Leu	synonymous_variant	Exon 8 of 10	1	NM_144585.4	ENSP00000366797.1		Q96S37-1

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50367

AN:

152034

Hom.:

10827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.605

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.260

AC:

61272

AN:

236058

Hom.:

9496

AF XY:

0.249

AC XY:

32029

AN XY:

128738

show subpopulations

Gnomad AFR exome

AF:

0.616

Gnomad AMR exome

AF:

0.240

Gnomad ASJ exome

AF:

0.173

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.198

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.216

AC:

314041

AN:

1453308

Hom.:

38840

Cov.:

AF XY:

0.214

AC XY:

154539

AN XY:

722840

show subpopulations

Gnomad4 AFR exome

AF:

0.617

Gnomad4 AMR exome

AF:

0.237

Gnomad4 ASJ exome

AF:

0.176

Gnomad4 EAS exome

AF:

0.477

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.277

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.241

GnomAD4 genome

AF:

0.332

AC:

50444

AN:

152152

Hom.:

10860

Cov.:

AF XY:

0.332

AC XY:

24694

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.606

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.167

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.298

Gnomad4 NFE

AF:

0.200

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.236

Hom.:

3815

Bravo

AF:

0.341

Asia WGS

AF:

0.350

AC:

1214

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dalmatian hypouricemia

Benign:2

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

5.6

DANN

Benign

0.53

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