5-36648340-T-C

Variant summary

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

The NM_004172.5(SLC1A3):c.319+18753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,062 control chromosomes in the GnomAD database, including 15,188 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 0.42 (15188 hom., cov: 32)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

SLC1A3 (HGNC:10941): (solute carrier family 1 member 3) This gene encodes a member of a member of a high affinity glutamate transporter family. This gene functions in the termination of excitatory neurotransmission in central nervous system. Mutations are associated with episodic ataxia, Type 6. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A3	NM_004172.5	c.319+18753T>C		intron_variant		ENST00000265113.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A3	ENST00000265113.9	c.319+18753T>C		intron_variant		1	NM_004172.5	P1
	ENST00000618632.1	n.33+975A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64123 AN: 151946 Hom.: 15187 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.422 AC: 64131 AN: 152062 Hom.: 15188 Cov.: 32 AF XY: 0.428 AC XY: 31835 AN XY: 74308

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.467

Alfa AF: 0.448 Hom.: 2102

Bravo AF: 0.410

Asia WGS AF: 0.497 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.64

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: rs891189; hg19: chr5-36648442;