19-14972983-C-T

Position:

• chr19-14972983-C-T

Variant summary

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

The NM_005071.3(SLC1A6):​c.-7-66G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,280,364 control chromosomes in the GnomAD database, including 180,485 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 0.53 (21404 hom., cov: 33)
  • Exomes 𝑓: 0.53 (159081 hom.)
• Consequence: SLC1A6 NM_005071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

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]

SLC1A6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A6	NM_005071.3	c.-7-66G>A		intron_variant		ENST00000594383.2	NP_005062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A6	ENST00000594383.2	c.-7-66G>A		intron_variant		2	NM_005071.3	ENSP00000472133.2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80099 AN: 151990 Hom.: 21392 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.494

GnomAD4 exome AF: 0.530 AC: 598150 AN: 1128256 Hom.: 159081 Cov.: 15 AF XY: 0.532 AC XY: 295244 AN XY: 554484

Gnomad4 AFR exome AF: 0.480

Gnomad4 AMR exome AF: 0.560

Gnomad4 ASJ exome AF: 0.382

Gnomad4 EAS exome AF: 0.684

Gnomad4 SAS exome AF: 0.603

Gnomad4 FIN exome AF: 0.580

Gnomad4 NFE exome AF: 0.521

Gnomad4 OTH exome AF: 0.519

GnomAD4 genome AF: 0.527 AC: 80150 AN: 152108 Hom.: 21404 Cov.: 33 AF XY: 0.533 AC XY: 39683 AN XY: 74384

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.491

Alfa AF: 0.460 Hom.: 2926

Bravo AF: 0.521

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8103212; hg19: chr19-15083795;