rs11128699

Positions:

• chr3-14454654-G-A
• chr3-14454654-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003043.6(SLC6A6):​c.600-3296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,038 control chromosomes in the GnomAD database, including 14,480 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 0.43 (14480 hom., cov: 33)
• Consequence: SLC6A6 NM_003043.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A6	NM_003043.6	c.600-3296G>A		intron_variant		ENST00000622186.5	NP_003034.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A6	ENST00000622186.5	c.600-3296G>A		intron_variant		1	NM_003043.6	ENSP00000480890.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65484 AN: 151920 Hom.: 14462 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65535 AN: 152038 Hom.: 14480 Cov.: 33 AF XY: 0.429 AC XY: 31865 AN XY: 74324

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.433

Alfa AF: 0.414 Hom.: 26347

Bravo AF: 0.431

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.014
DANN	Benign	0.55

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: rs11128699; hg19: chr3-14496162;