rs17237132

Positions:

• chr3-14457512-C-T

Variant summary

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

The NM_003043.6(SLC6A6):​c.600-438C>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_003043.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A6	NM_003043.6	c.600-438C>T		intron_variant		ENST00000622186.5	NP_003034.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A6	ENST00000622186.5	c.600-438C>T		intron_variant		1	NM_003043.6	ENSP00000480890	P1

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

Gnomad4 AFR AF: 0.0329

Gnomad4 AMR AF: 0.0584

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0315

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0398 Hom.: 32

Bravo AF: 0.0422

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.56

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: rs17237132; hg19: chr3-14499020;