5-36601753-T-C

Position:

• chr5-36601753-T-C

Variant summary

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

The ENST00000680318.1(SLC1A3):​c.-96+5075T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 150,704 control chromosomes in the GnomAD database, including 21,265 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 0.52 (21265 hom., cov: 26)
• Consequence: SLC1A3 ENST00000680318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36601753T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A3	ENST00000680318.1	c.-96+5075T>C		intron_variant				ENSP00000505057.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 78826 AN: 150594 Hom.: 21227 Cov.: 26

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.524 AC: 78906 AN: 150704 Hom.: 21265 Cov.: 26 AF XY: 0.519 AC XY: 38174 AN XY: 73510

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.482

Alfa AF: 0.487 Hom.: 17054

Bravo AF: 0.528

Asia WGS AF: 0.429 AC: 1493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2731877; hg19: chr5-36601855; COSMIC: COSV54316583;