rs2341984

Variant names:

• chr3-14486496-T-A
• rs2341984
• NM_003043.6:c.*1489T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-14486496-T-A
• chr3-14486496-T-C
• chr3-14486496-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003043.6(SLC6A6):​c.*1489T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SLC6A6 NM_003043.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 4 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: MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	NM_003043.6	MANE Select	c.*1489T>A		3_prime_UTR	Exon 15 of 15	NP_003034.2	P31641-1
	SLC6A6	NM_001134367.3		c.*1489T>A		3_prime_UTR	Exon 15 of 15	NP_001127839.2	Q59GD7
	SLC6A6	NR_103507.3		n.3522T>A		non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A6	ENST00000622186.5	TSL:1 MANE Select	c.*1489T>A		3_prime_UTR	Exon 15 of 15	ENSP00000480890.1	P31641-1
	SLC6A6	ENST00000613060.4	TSL:1	c.*1489T>A		3_prime_UTR	Exon 15 of 15	ENSP00000481625.1	A0A087WY96
	SLC6A6	ENST00000855618.1		c.*1489T>A		3_prime_UTR	Exon 14 of 14	ENSP00000525677.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.87

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: rs2341984; hg19: chr3-14528004;