Genetic Variant SLC6A6:c.*1489T>C (chr3-14486496-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_003043.6(SLC6A6):c.*1489T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,550 control chromosomes in the GnomAD database, including 34,533 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 0.67 ( 34389 hom., cov: 32)

Exomes 𝑓: 0.75 ( 144 hom. )

Consequence

SLC6A6
NM_003043.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.870

Publications

4 publications found

Variant links:

Genes affected

SLC6A6 (HGNC:11052): (solute carrier family 6 member 6) This gene encodes a multi-pass membrane protein that is a member of a family of sodium and chloride-ion dependent transporters. The encoded protein transports taurine and beta-alanine. There is a pseudogene for this gene on chromosome 21. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

SLC6A6 Gene-Disease associations (from GenCC):

hypotaurinemic retinal degeneration and cardiomyopathy
Inheritance: AR Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen

SLC6A6 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003043.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC6A6	NM_003043.6	MANE Select	c.*1489T>C	3_prime_UTR	Exon 15 of 15	NP_003034.2	P31641-1
SLC6A6	NM_001134367.3		c.*1489T>C	3_prime_UTR	Exon 15 of 15	NP_001127839.2	Q59GD7
SLC6A6	NR_103507.3		n.3522T>C	non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC6A6	ENST00000622186.5	TSL:1 MANE Select	c.*1489T>C	3_prime_UTR	Exon 15 of 15	ENSP00000480890.1	P31641-1
SLC6A6	ENST00000613060.4	TSL:1	c.*1489T>C	3_prime_UTR	Exon 15 of 15	ENSP00000481625.1	A0A087WY96
SLC6A6	ENST00000855618.1		c.*1489T>C	3_prime_UTR	Exon 14 of 14	ENSP00000525677.1

Frequencies

GnomAD3 genomes

AF:

0.667

AC:

101374

AN:

151934

Hom.:

34374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.697

Gnomad AMR

AF:

0.748

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.633

Gnomad FIN

AF:

0.746

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.701

Gnomad OTH

AF:

0.660

GnomAD4 exome

AF:

0.751

AC:

374

AN:

498

Hom.:

144

Cov.:

AF XY:

0.747

AC XY:

233

AN XY:

312

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.755

AC:

320

AN:

424

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.672

AC:

AN:

Other (OTH)

AF:

0.900

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.667

AC:

101432

AN:

152052

Hom.:

34389

Cov.:

AF XY:

0.671

AC XY:

49848

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.541

AC:

22435

AN:

41452

American (AMR)

AF:

0.748

AC:

11436

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.664

AC:

2305

AN:

3470

East Asian (EAS)

AF:

0.871

AC:

4504

AN:

5174

South Asian (SAS)

AF:

0.632

AC:

3047

AN:

4818

European-Finnish (FIN)

AF:

0.746

AC:

7867

AN:

10546

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.701

AC:

47653

AN:

67996

Other (OTH)

AF:

0.657

AC:

1384

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1704

3408

5111

6815

8519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.691

Hom.:

99273

Bravo

AF:

0.669

Asia WGS

AF:

0.727

AC:

2526

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

0.87

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