Variant rs955434 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000539841.1(SLC22A8):n.7091C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,134 control chromosomes in the GnomAD database, including 4,128 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 0.22 ( 4126 hom., cov: 32)

Exomes 𝑓: 0.25 ( 2 hom. )

Consequence

SLC22A8
ENST00000539841.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.500

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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A8	ENST00000539841.1 linkuse as main transcript	n.7091C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33866

AN:

151960

Hom.:

4114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.214

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.417

Gnomad4 NFE exome

AF:

0.211

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.223

AC:

33900

AN:

152078

Hom.:

4126

Cov.:

AF XY:

0.223

AC XY:

16593

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.262

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.234

Alfa

AF:

0.245

Hom.:

6188

Bravo

AF:

0.219

Asia WGS

AF:

0.290

AC:

1005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.0

DANN

Benign

0.69

Splicing

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