Variant 11-64598471-T-C 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_144585.4(SLC22A12):c.831-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 1,550,812 control chromosomes in the GnomAD database, including 347,784 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 23748 hom., cov: 33)

Exomes 𝑓: 0.67 ( 324036 hom. )

Consequence

SLC22A12
NM_144585.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -4.86

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 11-64598471-T-C is Benign according to our data. Variant chr11-64598471-T-C is described in ClinVar as [Benign]. Clinvar id is 1222614.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A12	NM_144585.4 linkuse as main transcript	c.831-45T>C		intron_variant		ENST00000377574.6	NP_653186.2	Q96S37-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A12	ENST00000377574.6 linkuse as main transcript	c.831-45T>C		intron_variant		1	NM_144585.4	ENSP00000366797.1		Q96S37-1

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77720

AN:

151976

Hom.:

23751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.834

Gnomad AMR

AF:

0.509

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.582

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.701

Gnomad OTH

AF:

0.557

GnomAD3 exomes

AF:

0.572

AC:

87926

AN:

153752

Hom.:

27376

AF XY:

0.587

AC XY:

48248

AN XY:

82178

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.457

Gnomad ASJ exome

AF:

0.711

Gnomad EAS exome

AF:

0.223

Gnomad SAS exome

AF:

0.605

Gnomad FIN exome

AF:

0.583

Gnomad NFE exome

AF:

0.706

Gnomad OTH exome

AF:

0.619

GnomAD4 exome

AF:

0.669

AC:

935606

AN:

1398718

Hom.:

324036

Cov.:

AF XY:

0.669

AC XY:

461929

AN XY:

690138

show subpopulations

Gnomad4 AFR exome

AF:

0.169

Gnomad4 AMR exome

AF:

0.460

Gnomad4 ASJ exome

AF:

0.709

Gnomad4 EAS exome

AF:

0.201

Gnomad4 SAS exome

AF:

0.604

Gnomad4 FIN exome

AF:

0.593

Gnomad4 NFE exome

AF:

0.716

Gnomad4 OTH exome

AF:

0.630

GnomAD4 genome

AF:

0.511

AC:

77728

AN:

152094

Hom.:

23748

Cov.:

AF XY:

0.505

AC XY:

37528

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.583

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.701

Gnomad4 OTH

AF:

0.559

Alfa

AF:

0.585

Hom.:

5982

Bravo

AF:

0.492

Asia WGS

AF:

0.385

AC:

1341

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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 12, 2018	- -

Dalmatian hypouricemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.39

DANN

Benign

0.40

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