rs6790433

Variant names:

• chr3-14439270-T-C
• rs6790433
• NM_003043.6:c.-11-4354T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-14439270-T-C
• chr3-14439270-T-G

Variant summary

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

The NM_003043.6(SLC6A6):​c.-11-4354T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,158 control chromosomes in the GnomAD database, including 6,412 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 0.29 (6412 hom., cov: 33)
• Consequence: SLC6A6 NM_003043.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A6	NM_003043.6	c.-11-4354T>C		intron_variant	Intron 2 of 14	ENST00000622186.5	NP_003034.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A6	ENST00000622186.5	c.-11-4354T>C		intron_variant	Intron 2 of 14	1	NM_003043.6	ENSP00000480890.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43764 AN: 152040 Hom.: 6406 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.288 AC: 43804 AN: 152158 Hom.: 6412 Cov.: 33 AF XY: 0.285 AC XY: 21194 AN XY: 74382

African (AFR) AF: 0.343 AC: 14232 AN: 41502

American (AMR) AF: 0.210 AC: 3210 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5164

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4826

European-Finnish (FIN) AF: 0.227 AC: 2406 AN: 10584

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19381 AN: 67990

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.287 Hom.: 13487

Bravo AF: 0.289

Asia WGS AF: 0.304 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.67
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: rs6790433; hg19: chr3-14480778;