rs17237132

Variant names:

• chr3-14457512-C-T
• rs17237132
• NM_003043.6:c.600-438C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134367.3(SLC6A6):​c.903-438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0416 in 152,246 control chromosomes in the GnomAD database, including 145 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 0.042 (145 hom., cov: 33)
• Consequence: SLC6A6 NM_001134367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 3 publications found

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: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134367.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	NM_003043.6	MANE Select	c.600-438C>T		intron	N/A	NP_003034.2
	SLC6A6	NM_001134367.3		c.903-438C>T		intron	N/A	NP_001127839.2
	SLC6A6	NR_103507.3		n.895-438C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	ENST00000622186.5	TSL:1 MANE Select	c.600-438C>T		intron	N/A	ENSP00000480890.1
	SLC6A6	ENST00000613060.4	TSL:1	c.903-438C>T		intron	N/A	ENSP00000481625.1
	SLC6A6	ENST00000622176.4	TSL:1	n.*637-438C>T		intron	N/A	ENSP00000482220.1

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6344 AN: 152128 Hom.: 145 Cov.: 33

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0517

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0416 AC: 6341 AN: 152246 Hom.: 145 Cov.: 33 AF XY: 0.0427 AC XY: 3180 AN XY: 74442

African (AFR) AF: 0.0329 AC: 1365 AN: 41548

American (AMR) AF: 0.0584 AC: 894 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0593 AC: 206 AN: 3472

East Asian (EAS) AF: 0.0545 AC: 282 AN: 5176

South Asian (SAS) AF: 0.101 AC: 486 AN: 4822

European-Finnish (FIN) AF: 0.0315 AC: 334 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2640 AN: 68008

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0405 Hom.: 77

Bravo AF: 0.0422

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.56
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17237132; hg19: chr3-14499020;