3-14486910-G-A

Variant names:

• chr3-14486910-G-A
• rs11713355
• NM_003043.6:c.*1903G>A

Variant summary

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

The NM_003043.6(SLC6A6):​c.*1903G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,188 control chromosomes in the GnomAD database, including 2,255 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 0.17 (2255 hom., cov: 33)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: SLC6A6 NM_003043.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	NM_003043.6	MANE Select	c.*1903G>A		3_prime_UTR	Exon 15 of 15	NP_003034.2
	SLC6A6	NR_103507.3		n.3936G>A		non_coding_transcript_exon	Exon 14 of 14
	SLC6A6	NM_001134367.3		c.*1903G>A		3_prime_UTR	Exon 15 of 15	NP_001127839.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	ENST00000622186.5	TSL:1 MANE Select	c.*1903G>A		3_prime_UTR	Exon 15 of 15	ENSP00000480890.1
	SLC6A6	ENST00000613060.4	TSL:1	c.*1903G>A		3_prime_UTR	Exon 15 of 15	ENSP00000481625.1
	SLC6A6	ENST00000618278.4	TSL:5	n.*2561G>A		non_coding_transcript_exon	Exon 14 of 14	ENSP00000481946.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25280 AN: 152040 Hom.: 2253 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.167 AC: 5 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 4 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 2 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.166 AC: 25307 AN: 152158 Hom.: 2255 Cov.: 33 AF XY: 0.163 AC XY: 12105 AN XY: 74400

African (AFR) AF: 0.128 AC: 5308 AN: 41512

American (AMR) AF: 0.149 AC: 2275 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.0937 AC: 485 AN: 5174

South Asian (SAS) AF: 0.151 AC: 727 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1474 AN: 10600

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13662 AN: 67982

Other (OTH) AF: 0.194 AC: 409 AN: 2106

Alfa AF: 0.185 Hom.: 5615

Bravo AF: 0.162

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.98
DANN	Benign	0.58
PhyloP100		-0.13
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: rs11713355; hg19: chr3-14528418;