Variant 11-64591337-G-A 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.-220G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 607,996 control chromosomes in the GnomAD database, including 117,656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 23372 hom., cov: 33)

Exomes 𝑓: 0.62 ( 94284 hom. )

Consequence

SLC22A12
NM_144585.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.96

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 11-64591337-G-A is Benign according to our data. Variant chr11-64591337-G-A is described in ClinVar as [Benign]. Clinvar id is 305225.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A12	NM_144585.4 link	c.-220G>A		5_prime_UTR_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 link	c.-220G>A		5_prime_UTR_variant	1/10	1	NM_144585.4	ENSP00000366797.1		Q96S37-1

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

77242

AN:

152010

Hom.:

23376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.834

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.695

Gnomad OTH

AF:

0.554

GnomAD4 exome

AF:

0.625

AC:

284737

AN:

455868

Hom.:

94284

Cov.:

AF XY:

0.626

AC XY:

149183

AN XY:

238336

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.475

Gnomad4 ASJ exome

AF:

0.710

Gnomad4 EAS exome

AF:

0.199

Gnomad4 SAS exome

AF:

0.591

Gnomad4 FIN exome

AF:

0.597

Gnomad4 NFE exome

AF:

0.703

Gnomad4 OTH exome

AF:

0.617

GnomAD4 genome

AF:

0.508

AC:

77249

AN:

152128

Hom.:

23372

Cov.:

AF XY:

0.501

AC XY:

37289

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.573

Gnomad4 FIN

AF:

0.571

Gnomad4 NFE

AF:

0.695

Gnomad4 OTH

AF:

0.555

Alfa

AF:

0.574

Hom.:

4852

Bravo

AF:

0.489

Asia WGS

AF:

0.379

AC:

1321

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

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.081

DANN

Benign

0.61

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