Genetic Variant SLC22A8:c.1002-194G>A (chr11-62994950-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004254.4(SLC22A8):c.1002-194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 620,388 control chromosomes in the GnomAD database, including 18,333 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 ( 5842 hom., cov: 32)

Exomes 𝑓: 0.22 ( 12491 hom. )

Consequence

SLC22A8
NM_004254.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A8	NM_004254.4 link	c.1002-194G>A		intron_variant	Intron 7 of 10	ENST00000336232.7	NP_004245.2	Q8TCC7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A8	ENST00000336232.7 link	c.1002-194G>A		intron_variant	Intron 7 of 10	1	NM_004254.4	ENSP00000337335.2		Q8TCC7-1

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39840

AN:

151946

Hom.:

5804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.329

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.249

GnomAD4 exome

AF:

0.224

AC:

104914

AN:

468324

Hom.:

12491

Cov.:

AF XY:

0.219

AC XY:

54567

AN XY:

248654

show subpopulations

Gnomad4 AFR exome

AF:

0.376

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.335

Gnomad4 SAS exome

AF:

0.156

Gnomad4 FIN exome

AF:

0.241

Gnomad4 NFE exome

AF:

0.225

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.263

AC:

39925

AN:

152064

Hom.:

5842

Cov.:

AF XY:

0.261

AC XY:

19398

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.377

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.327

Gnomad4 SAS

AF:

0.166

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.224

Hom.:

5476

Bravo

AF:

0.264

Asia WGS

AF:

0.237

AC:

824

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.10

DANN

Benign

0.47

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