rs11713355

Positions:

• chr3-14486910-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A6	NM_003043.6	c.*1903G>A		3_prime_UTR_variant	15/15	ENST00000622186.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A6	ENST00000622186.5	c.*1903G>A		3_prime_UTR_variant	15/15	1	NM_003043.6	P1
SLC6A6	ENST00000613060.4	c.*1903G>A		3_prime_UTR_variant	15/15	1
SLC6A6	ENST00000618278.4	c.*2561G>A		3_prime_UTR_variant, NMD_transcript_variant	14/14	5
SLC6A6	ENST00000649500.1	c.*3674G>A		3_prime_UTR_variant, NMD_transcript_variant	15/15

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

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.214

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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0937

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.194

Alfa AF: 0.189 Hom.: 3662

Bravo AF: 0.162

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.98
DANN	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs11713355; hg19: chr3-14528418;