dbSNP rs10897312: SLC22A6:c.369+136C>T (chr11-62984186-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_153276.3(SLC22A6):c.369+136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,279,986 control chromosomes in the GnomAD database, including 10,387 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 0.17 ( 3086 hom., cov: 31)

Exomes 𝑓: 0.10 ( 7301 hom. )

Consequence

SLC22A6
NM_153276.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340

Publications

6 publications found

Variant links:

Genes affected

SLC22A6 (HGNC:10970): (solute carrier family 22 member 6) The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SLC22A6 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A6	NM_153276.3 link	c.369+136C>T		intron_variant	Intron 1 of 9	ENST00000360421.9	NP_695008.1	Q4U2R8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A6	ENST00000360421.9 link	c.369+136C>T		intron_variant	Intron 1 of 9	1	NM_153276.3	ENSP00000353597.4		Q4U2R8-2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25361

AN:

151696

Hom.:

3059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.0840

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.147

Gnomad NFE

AF:

0.0853

Gnomad OTH

AF:

0.151

GnomAD4 exome

AF:

0.0995

AC:

112260

AN:

1128194

Hom.:

7301

Cov.:

AF XY:

0.101

AC XY:

56517

AN XY:

560234

show subpopulations

African (AFR)

AF:

0.348

AC:

8645

AN:

24816

American (AMR)

AF:

0.121

AC:

2891

AN:

23848

Ashkenazi Jewish (ASJ)

AF:

0.0870

AC:

1657

AN:

19052

East Asian (EAS)

AF:

0.232

AC:

8020

AN:

34550

South Asian (SAS)

AF:

0.163

AC:

10137

AN:

62198

European-Finnish (FIN)

AF:

0.101

AC:

4706

AN:

46594

Middle Eastern (MID)

AF:

0.183

AC:

892

AN:

4876

European-Non Finnish (NFE)

AF:

0.0807

AC:

69686

AN:

863904

Other (OTH)

AF:

0.116

AC:

5626

AN:

48356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

5081

10162

15243

20324

25405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2602

5204

7806

10408

13010

<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:

0.168

AC:

25436

AN:

151792

Hom.:

3086

Cov.:

AF XY:

0.167

AC XY:

12417

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.335

AC:

13862

AN:

41388

American (AMR)

AF:

0.118

AC:

1795

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0840

AC:

291

AN:

3466

East Asian (EAS)

AF:

0.244

AC:

1250

AN:

5118

South Asian (SAS)

AF:

0.175

AC:

842

AN:

4804

European-Finnish (FIN)

AF:

0.108

AC:

1133

AN:

10470

Middle Eastern (MID)

AF:

0.141

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0853

AC:

5801

AN:

67968

Other (OTH)

AF:

0.156

AC:

328

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

974

1948

2922

3896

4870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.112

Hom.:

2530

Bravo

AF:

0.177

Asia WGS

AF:

0.213

AC:

741

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.7

(source)

DANN

Benign

0.54

PhyloP100

0.034

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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