5-36636737-A-T

Position:

• chr5-36636737-A-T

Variant summary

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

The NM_004172.5(SLC1A3):​c.319+7150A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,552 control chromosomes in the GnomAD database, including 1,410 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 0.12 (1410 hom., cov: 29)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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]

ENSG00000274441 (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 (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A3	NM_004172.5	c.319+7150A>T		intron_variant		ENST00000265113.9	NP_004163.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A3	ENST00000265113.9	c.319+7150A>T		intron_variant		1	NM_004172.5	ENSP00000265113.4

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18704 AN: 151438 Hom.: 1408 Cov.: 29

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.123 AC: 18710 AN: 151552 Hom.: 1410 Cov.: 29 AF XY: 0.123 AC XY: 9099 AN XY: 74028

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.128

Alfa AF: 0.135 Hom.: 201

Bravo AF: 0.118

Asia WGS AF: 0.125 AC: 437 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
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: rs7734056; hg19: chr5-36636839;