Genetic Variant SLC10A6:c.496+40G>A (chr4-86833266-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 NM_197965.3(SLC10A6):c.496+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,428,856 control chromosomes in the GnomAD database, including 17,982 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 0.14 ( 1768 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16214 hom. )

Consequence

SLC10A6
NM_197965.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.149

Publications

10 publications found

Variant links:

Genes affected

SLC10A6 (HGNC:30603): (solute carrier family 10 member 6) Predicted to enable bile acid:sodium symporter activity. Predicted to be involved in bile acid and bile salt transport. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC10A6 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC10A6	NM_197965.3 link	c.496+40G>A		intron_variant	Intron 2 of 5	ENST00000273905.7	NP_932069.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC10A6	ENST00000273905.7 link	c.496+40G>A		intron_variant	Intron 2 of 5	1	NM_197965.3	ENSP00000273905.6
SLC10A6	ENST00000505535.1 link	n.505+40G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22018

AN:

151952

Hom.:

1764

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0889

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.152

GnomAD2 exomes

AF:

0.169

AC:

41250

AN:

244162

AF XY:

0.163

show subpopulations

Gnomad AFR exome

AF:

0.0840

Gnomad AMR exome

AF:

0.246

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.276

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.152

AC:

194464

AN:

1276786

Hom.:

16214

Cov.:

AF XY:

0.150

AC XY:

96813

AN XY:

643884

show subpopulations

African (AFR)

AF:

0.0857

AC:

2533

AN:

29542

American (AMR)

AF:

0.235

AC:

10004

AN:

42622

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

3336

AN:

24580

East Asian (EAS)

AF:

0.302

AC:

11672

AN:

38654

South Asian (SAS)

AF:

0.103

AC:

8276

AN:

80306

European-Finnish (FIN)

AF:

0.205

AC:

10857

AN:

53046

Middle Eastern (MID)

AF:

0.139

AC:

748

AN:

5366

European-Non Finnish (NFE)

AF:

0.146

AC:

138724

AN:

948556

Other (OTH)

AF:

0.154

AC:

8314

AN:

54114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

7544

15088

22631

30175

37719

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4738

9476

14214

18952

23690

<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:

0.145

AC:

22033

AN:

152070

Hom.:

1768

Cov.:

AF XY:

0.149

AC XY:

11096

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.0887

AC:

3684

AN:

41512

American (AMR)

AF:

0.197

AC:

3013

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

476

AN:

3472

East Asian (EAS)

AF:

0.274

AC:

1411

AN:

5158

South Asian (SAS)

AF:

0.113

AC:

542

AN:

4810

European-Finnish (FIN)

AF:

0.213

AC:

2252

AN:

10560

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10084

AN:

67968

Other (OTH)

AF:

0.156

AC:

328

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

950

1900

2851

3801

4751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.150

Hom.:

6195

Bravo

AF:

0.143

Asia WGS

AF:

0.169

AC:

588

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.1

(source)

DANN

Benign

0.64

PhyloP100

0.15

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