5-36618301-A-G

Position:

• chr5-36618301-A-G

Variant summary

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

The NM_004172.5(SLC1A3):​c.181+9697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,206 control chromosomes in the GnomAD database, including 3,032 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 0.16 (3032 hom., cov: 33)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

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]

SLC1A3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A3	NM_004172.5	c.181+9697A>G		intron_variant		ENST00000265113.9	NP_004163.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A3	ENST00000265113.9	c.181+9697A>G		intron_variant		1	NM_004172.5	ENSP00000265113.4

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24138 AN: 152088 Hom.: 3028 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.159 AC: 24169 AN: 152206 Hom.: 3032 Cov.: 33 AF XY: 0.158 AC XY: 11748 AN XY: 74428

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0881 Hom.: 1097

Bravo AF: 0.167

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.91
DANN	Benign	0.85

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: rs6451304; hg19: chr5-36618403;