Variant rs7929627 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.1286-103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 927,968 control chromosomes in the GnomAD database, including 32,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 10869 hom., cov: 33)

Exomes 𝑓: 0.22 ( 21276 hom. )

Consequence

SLC22A12
NM_144585.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.435

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=-0.92).

BP6

Variant 11-64600264-A-G is Benign according to our data. Variant chr11-64600264-A-G is described in ClinVar as [Benign]. Clinvar id is 1262572.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 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.1286-103A>G		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.1286-103A>G		intron_variant		1	NM_144585.4	ENSP00000366797.1		Q96S37-1

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50381

AN:

151988

Hom.:

10836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.606

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.288

GnomAD4 exome

AF:

0.215

AC:

166845

AN:

775862

Hom.:

21276

AF XY:

0.213

AC XY:

86163

AN XY:

405088

show subpopulations

Gnomad4 AFR exome

AF:

0.597

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.475

Gnomad4 SAS exome

AF:

0.209

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.240

GnomAD4 genome

AF:

0.332

AC:

50458

AN:

152106

Hom.:

10869

Cov.:

AF XY:

0.332

AC XY:

24693

AN XY:

74346

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:

0.219

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.200

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.317

Hom.:

1477

Bravo

AF:

0.341

Asia WGS

AF:

0.351

AC:

1220

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.8

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