Genetic Variant SLCO6A1:c.802+142A>G (chr5-102477534-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 ENST00000506729.6(SLCO6A1):c.802+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 610,780 control chromosomes in the GnomAD database, including 124,768 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 0.64 ( 31037 hom., cov: 32)

Exomes 𝑓: 0.64 ( 93731 hom. )

Consequence

SLCO6A1
ENST00000506729.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.772

Publications

6 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=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506729.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLCO6A1	NM_173488.5	MANE Select	c.802+142A>G	intron	N/A	NP_775759.3
SLCO6A1	NM_001289002.2		c.802+142A>G	intron	N/A	NP_001275931.1
SLCO6A1	NM_001289004.2		c.617-1741A>G	intron	N/A	NP_001275933.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLCO6A1	ENST00000506729.6	TSL:1 MANE Select	c.802+142A>G	intron	N/A	ENSP00000421339.1
SLCO6A1	ENST00000379807.7	TSL:1	c.802+142A>G	intron	N/A	ENSP00000369135.3
SLCO6A1	ENST00000389019.7	TSL:1	c.617-1741A>G	intron	N/A	ENSP00000373671.3

Frequencies

GnomAD3 genomes

AF:

0.637

AC:

96777

AN:

151874

Hom.:

31015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.656

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.732

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.639

Gnomad OTH

AF:

0.622

GnomAD4 exome

AF:

0.635

AC:

291375

AN:

458788

Hom.:

93731

AF XY:

0.635

AC XY:

149807

AN XY:

236100

show subpopulations

African (AFR)

AF:

0.672

AC:

8453

AN:

12570

American (AMR)

AF:

0.583

AC:

9613

AN:

16494

Ashkenazi Jewish (ASJ)

AF:

0.725

AC:

8935

AN:

12322

East Asian (EAS)

AF:

0.461

AC:

13810

AN:

29930

South Asian (SAS)

AF:

0.630

AC:

16357

AN:

25956

European-Finnish (FIN)

AF:

0.710

AC:

22897

AN:

32242

Middle Eastern (MID)

AF:

0.619

AC:

1313

AN:

2122

European-Non Finnish (NFE)

AF:

0.643

AC:

194234

AN:

302108

Other (OTH)

AF:

0.629

AC:

15763

AN:

25044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5006

10011

15017

20022

25028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2382

4764

7146

9528

11910

<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:

0.637

AC:

96841

AN:

151992

Hom.:

31037

Cov.:

AF XY:

0.640

AC XY:

47551

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.656

AC:

27200

AN:

41446

American (AMR)

AF:

0.572

AC:

8719

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

2435

AN:

3470

East Asian (EAS)

AF:

0.458

AC:

2360

AN:

5156

South Asian (SAS)

AF:

0.593

AC:

2861

AN:

4824

European-Finnish (FIN)

AF:

0.732

AC:

7735

AN:

10566

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.639

AC:

43430

AN:

67960

Other (OTH)

AF:

0.617

AC:

1303

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1782

3564

5345

7127

8909

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<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:

0.652

Hom.:

4164

Bravo

AF:

0.630

Asia WGS

AF:

0.525

AC:

1823

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.77

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over