rs873599

Variant names:

• chr19-14958048-A-T
• rs873599
• NM_005071.3:c.936-1339T>A

Variant summary

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

The NM_005071.3(SLC1A6):​c.936-1339T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,006 control chromosomes in the GnomAD database, including 35,392 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 0.68 (35392 hom., cov: 31)
• Consequence: SLC1A6 NM_005071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 1 publications found

Genes affected

SLC1A6 (HGNC:10944): (solute carrier family 1 member 6) Predicted to enable high-affinity glutamate transmembrane transporter activity. Involved in neurotransmitter uptake. Located in intermediate filament cytoskeleton and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005071.3. 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
	SLC1A6	NM_005071.3	MANE Select	c.936-1339T>A		intron	N/A	NP_005062.1
	SLC1A6	NM_001384669.1		c.936-1339T>A		intron	N/A	NP_001371598.1
	SLC1A6	NR_073589.2		n.897-1339T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A6	ENST00000594383.2	TSL:2 MANE Select	c.936-1339T>A		intron	N/A	ENSP00000472133.2
	SLC1A6	ENST00000221742.7	TSL:1	c.936-1339T>A		intron	N/A	ENSP00000221742.3
	SLC1A6	ENST00000600144.5	TSL:1	c.936-3719T>A		intron	N/A	ENSP00000471038.1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103508 AN: 151888 Hom.: 35361 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.681 AC: 103592 AN: 152006 Hom.: 35392 Cov.: 31 AF XY: 0.685 AC XY: 50851 AN XY: 74270

African (AFR) AF: 0.736 AC: 30516 AN: 41468

American (AMR) AF: 0.660 AC: 10076 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1708 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3681 AN: 5150

South Asian (SAS) AF: 0.707 AC: 3403 AN: 4812

European-Finnish (FIN) AF: 0.700 AC: 7392 AN: 10560

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44629 AN: 67968

Other (OTH) AF: 0.652 AC: 1378 AN: 2114

Alfa AF: 0.678 Hom.: 4358

Bravo AF: 0.679

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.81
PhyloP100		-0.22
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: rs873599; hg19: chr19-15068860;