5-36605258-C-T

Position:

• chr5-36605258-C-T

Variant summary

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

The ENST00000680318.1(SLC1A3):​c.-95-3071C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,178 control chromosomes in the GnomAD database, including 56,684 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 0.86 (56684 hom., cov: 31)
• Consequence: SLC1A3 ENST00000680318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A3	ENST00000680318.1	c.-95-3071C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130750 AN: 152060 Hom.: 56612 Cov.: 31

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.860 AC: 130882 AN: 152178 Hom.: 56684 Cov.: 31 AF XY: 0.861 AC XY: 64040 AN XY: 74390

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.860

Alfa AF: 0.819 Hom.: 67944

Bravo AF: 0.870

Asia WGS AF: 0.905 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2562582; hg19: chr5-36605360;