dbSNP rs2276300: SLC22A6:c.921+33C>T (chr11-62981227-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.921+33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,608,726 control chromosomes in the GnomAD database, including 612 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 0.0076 ( 94 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 518 hom. )

Consequence

SLC22A6
NM_153276.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.782

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A6	NM_153276.3 link	c.921+33C>T		intron_variant	Intron 5 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.921+33C>T		intron_variant	Intron 5 of 9	1	NM_153276.3	ENSP00000353597.4		Q4U2R8-2

Frequencies

GnomAD3 genomes

AF:

0.00755

AC:

1149

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00294

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.00717

GnomAD2 exomes

AF:

0.0154

AC:

3700

AN:

239752

AF XY:

0.0148

show subpopulations

Gnomad AFR exome

AF:

0.000327

Gnomad AMR exome

AF:

0.00129

Gnomad ASJ exome

AF:

0.00204

Gnomad EAS exome

AF:

0.179

Gnomad FIN exome

AF:

0.00232

Gnomad NFE exome

AF:

0.00120

Gnomad OTH exome

AF:

0.00930

GnomAD4 exome

AF:

0.00569

AC:

8291

AN:

1456380

Hom.:

518

Cov.:

AF XY:

0.00578

AC XY:

4188

AN XY:

723942

show subpopulations

African (AFR)

AF:

0.000180

AC:

AN:

33410

American (AMR)

AF:

0.00123

AC:

AN:

43896

Ashkenazi Jewish (ASJ)

AF:

0.00227

AC:

AN:

25966

East Asian (EAS)

AF:

0.153

AC:

6048

AN:

39492

South Asian (SAS)

AF:

0.00774

AC:

659

AN:

85090

European-Finnish (FIN)

AF:

0.00253

AC:

134

AN:

53066

Middle Eastern (MID)

AF:

0.00156

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.000676

AC:

750

AN:

1109492

Other (OTH)

AF:

0.00950

AC:

572

AN:

60202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

406

811

1217

1622

2028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

118

236

354

472

590

<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:

0.00759

AC:

1156

AN:

152346

Hom.:

Cov.:

AF XY:

0.00869

AC XY:

647

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.000385

AC:

AN:

41588

American (AMR)

AF:

0.00294

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00231

AC:

AN:

3470

East Asian (EAS)

AF:

0.174

AC:

899

AN:

5172

South Asian (SAS)

AF:

0.0126

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00320

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00103

AC:

AN:

68040

Other (OTH)

AF:

0.0109

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

146

195

244

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.00205

Hom.:

Bravo

AF:

0.00928

Asia WGS

AF:

0.0670

AC:

232

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.8

(source)

DANN

Benign

0.62

PhyloP100

-0.78

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