Genetic Variant SLC51B:c.188+143C>T (chr15-65051748-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_178859.4(SLC51B):c.188+143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 642,918 control chromosomes in the GnomAD database, including 57,249 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 0.36 ( 11042 hom., cov: 30)

Exomes 𝑓: 0.41 ( 46207 hom. )

Consequence

SLC51B
NM_178859.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326

Publications

5 publications found

Variant links:

Genes affected

SLC51B (HGNC:29956): (SLC51 subunit beta) Predicted to enable protein heterodimerization activity and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC51B links:

RASL12 (HGNC:30289): (RAS like family 12) Predicted to enable GDP binding activity; GTP binding activity; and GTPase activity. Predicted to be involved in signal transduction. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RASL12 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC51B	NM_178859.4 link	c.188+143C>T	intron_variant	Intron 3 of 3	ENST00000334287.3	NP_849190.2	Q86UW2
RASL12	XM_017022296.2 link	c.*242G>A	3_prime_UTR_variant	Exon 5 of 5		XP_016877785.1
RASL12	XM_005254434.5 link	c.426-6004G>A	intron_variant	Intron 4 of 4		XP_005254491.1
SLC51B	XM_005254159.6 link	c.188+143C>T	intron_variant	Intron 3 of 3		XP_005254216.1	Q86UW2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC51B	ENST00000334287.3 link	c.188+143C>T		intron_variant	Intron 3 of 3	2	NM_178859.4	ENSP00000335292.2		Q86UW2

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

54338

AN:

149276

Hom.:

11029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.784

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.402

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.415

AC:

204671

AN:

493524

Hom.:

46207

AF XY:

0.411

AC XY:

107273

AN XY:

261148

show subpopulations

African (AFR)

AF:

0.187

AC:

2419

AN:

12940

American (AMR)

AF:

0.485

AC:

9586

AN:

19782

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

4782

AN:

13604

East Asian (EAS)

AF:

0.809

AC:

23682

AN:

29278

South Asian (SAS)

AF:

0.337

AC:

16637

AN:

49360

European-Finnish (FIN)

AF:

0.408

AC:

15569

AN:

38154

Middle Eastern (MID)

AF:

0.347

AC:

863

AN:

2484

European-Non Finnish (NFE)

AF:

0.399

AC:

120520

AN:

301696

Other (OTH)

AF:

0.405

AC:

10613

AN:

26226

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5234

10467

15701

20934

26168

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1340

2680

4020

5360

6700

<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:

0.364

AC:

54366

AN:

149394

Hom.:

11042

Cov.:

AF XY:

0.370

AC XY:

26965

AN XY:

72866

show subpopulations

African (AFR)

AF:

0.195

AC:

7770

AN:

39864

American (AMR)

AF:

0.460

AC:

6932

AN:

15058

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1169

AN:

3430

East Asian (EAS)

AF:

0.784

AC:

4019

AN:

5128

South Asian (SAS)

AF:

0.352

AC:

1636

AN:

4652

European-Finnish (FIN)

AF:

0.424

AC:

4394

AN:

10374

Middle Eastern (MID)

AF:

0.380

AC:

111

AN:

292

European-Non Finnish (NFE)

AF:

0.402

AC:

27156

AN:

67630

Other (OTH)

AF:

0.382

AC:

787

AN:

2060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1638

3275

4913

6550

8188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.374

Hom.:

2663

Bravo

AF:

0.360

Asia WGS

AF:

0.505

AC:

1751

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

(source)

DANN

Benign

0.63

PhyloP100

0.33

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