Variant rs4149182 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004254.4(SLC22A8):c.437+79G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,018,738 control chromosomes in the GnomAD database, including 28,287 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5870 hom., cov: 31)

Exomes 𝑓: 0.22 ( 22417 hom. )

Consequence

SLC22A8
NM_004254.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

Variant links:

Genes affected

SLC22A8 (HGNC:10972): (solute carrier family 22 member 8) This gene encodes a protein involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and appears to be localized to the basolateral membrane of the kidney. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, May 2010]

SLC22A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A8	NM_004254.4 linkuse as main transcript	c.437+79G>C		intron_variant		ENST00000336232.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A8	ENST00000336232.7 linkuse as main transcript	c.437+79G>C		intron_variant		1	NM_004254.4	P1	Q8TCC7-1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39949

AN:

151790

Hom.:

5832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.328

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.249

GnomAD4 exome

AF:

0.221

AC:

191636

AN:

866830

Hom.:

22417

AF XY:

0.217

AC XY:

97596

AN XY:

449026

show subpopulations

Gnomad4 AFR exome

AF:

0.383

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.335

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.221

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.264

AC:

40038

AN:

151908

Hom.:

5870

Cov.:

AF XY:

0.262

AC XY:

19446

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.380

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.328

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.240

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.136

Hom.:

272

Bravo

AF:

0.265

Asia WGS

AF:

0.238

AC:

828

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.46

DANN

Benign

0.52

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over