dbSNP rs953894: SLC22A8:n.1782G>A (chr11-62994950-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000539841.1(SLC22A8):n.1782G>A 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 0.233 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
ENST00000539841.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

7 publications found

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:

ENSG00000301851 (HGNC:):

ENSG00000301851 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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

African (AFR)

AF:

0.376

AC:

5054

AN:

13426

American (AMR)

AF:

0.128

AC:

3267

AN:

25550

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

2711

AN:

14660

East Asian (EAS)

AF:

0.335

AC:

10335

AN:

30832

South Asian (SAS)

AF:

0.156

AC:

7773

AN:

49714

European-Finnish (FIN)

AF:

0.241

AC:

7204

AN:

29902

Middle Eastern (MID)

AF:

0.258

AC:

524

AN:

2028

European-Non Finnish (NFE)

AF:

0.225

AC:

61997

AN:

275536

Other (OTH)

AF:

0.227

AC:

6049

AN:

26676

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

4230

8459

12689

16918

21148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

384

768

1152

1536

1920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.263

AC:

39925

AN:

152064

Hom.:

5842

Cov.:

AF XY:

0.261

AC XY:

19398

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.377

AC:

15635

AN:

41454

American (AMR)

AF:

0.172

AC:

2627

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

644

AN:

3464

East Asian (EAS)

AF:

0.327

AC:

1690

AN:

5170

South Asian (SAS)

AF:

0.166

AC:

800

AN:

4812

European-Finnish (FIN)

AF:

0.241

AC:

2549

AN:

10584

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.222

AC:

15081

AN:

67970

Other (OTH)

AF:

0.253

AC:

533

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1464

2928

4393

5857

7321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.228

Hom.:

7193

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

(source)

DANN

Benign

0.47

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over