dbSNP rs10073892: SLCO6A1:c.1815-21A>G (chr5-102391066-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_173488.5(SLCO6A1):c.1815-21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,603,818 control chromosomes in the GnomAD database, including 57,670 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 0.21 ( 4580 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53090 hom. )

Consequence

SLCO6A1
NM_173488.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.634

Publications

14 publications found

Variant links:

Genes affected

SLCO6A1 (HGNC:23613): (solute carrier organic anion transporter family member 6A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO6A1 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5 link	c.1815-21A>G		intron_variant	Intron 10 of 13	ENST00000506729.6	NP_775759.3	Q86UG4-1A0A140VJU7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6 link	c.1815-21A>G		intron_variant	Intron 10 of 13	1	NM_173488.5	ENSP00000421339.1		Q86UG4-1

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32547

AN:

151962

Hom.:

4584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0515

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.203

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.240

GnomAD2 exomes

AF:

0.244

AC:

60996

AN:

250326

AF XY:

0.248

show subpopulations

Gnomad AFR exome

AF:

0.0454

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.364

Gnomad EAS exome

AF:

0.132

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.263

AC:

381541

AN:

1451738

Hom.:

53090

Cov.:

AF XY:

0.262

AC XY:

189351

AN XY:

722998

show subpopulations

African (AFR)

AF:

0.0481

AC:

1603

AN:

33310

American (AMR)

AF:

0.167

AC:

7468

AN:

44662

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

9258

AN:

26030

East Asian (EAS)

AF:

0.133

AC:

5261

AN:

39566

South Asian (SAS)

AF:

0.182

AC:

15621

AN:

86014

European-Finnish (FIN)

AF:

0.405

AC:

21632

AN:

53392

Middle Eastern (MID)

AF:

0.282

AC:

1618

AN:

5730

European-Non Finnish (NFE)

AF:

0.275

AC:

303408

AN:

1102984

Other (OTH)

AF:

0.261

AC:

15672

AN:

60050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

13503

27005

40508

54010

67513

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9806

19612

29418

39224

49030

<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:

0.214

AC:

32537

AN:

152080

Hom.:

4580

Cov.:

AF XY:

0.221

AC XY:

16387

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.0514

AC:

2137

AN:

41556

American (AMR)

AF:

0.202

AC:

3085

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

1219

AN:

3470

East Asian (EAS)

AF:

0.131

AC:

675

AN:

5160

South Asian (SAS)

AF:

0.176

AC:

849

AN:

4822

European-Finnish (FIN)

AF:

0.436

AC:

4602

AN:

10548

Middle Eastern (MID)

AF:

0.257

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.282

AC:

19161

AN:

67960

Other (OTH)

AF:

0.241

AC:

509

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1220

2440

3661

4881

6101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.255

Hom.:

16887

Bravo

AF:

0.190

Asia WGS

AF:

0.159

AC:

553

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.5

(source)

DANN

Benign

0.53

PhyloP100

0.63

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