rs873599

chr19-14958048-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A6	NM_005071.3	c.936-1339T>A		intron_variant		ENST00000594383.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A6	ENST00000594383.2	c.936-1339T>A		intron_variant		2	NM_005071.3	P1
SLC1A6	ENST00000221742.7	c.936-1339T>A		intron_variant		1		P1
SLC1A6	ENST00000600144.5	c.936-3719T>A		intron_variant		1
SLC1A6	ENST00000430939.6	c.744-1339T>A		intron_variant		2

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

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.652

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.2
Dann	Benign	0.81

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: rs873599; hg19: chr19-15068860;