5-36616433-A-G

Position:

• chr5-36616433-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+7829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,160 control chromosomes in the GnomAD database, including 50,632 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 0.81 (50632 hom., cov: 32)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511

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=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A3	NM_004172.5	c.181+7829A>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+7829A>G		intron_variant		1	NM_004172.5	ENSP00000265113.4

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123297 AN: 152042 Hom.: 50574 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.811 AC: 123413 AN: 152160 Hom.: 50632 Cov.: 32 AF XY: 0.815 AC XY: 60651 AN XY: 74386

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.813

Alfa AF: 0.747 Hom.: 52058

Bravo AF: 0.818

Asia WGS AF: 0.917 AC: 3187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	5.6
DANN	Benign	0.50

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: rs1366638; hg19: chr5-36616535; COSMIC: COSV54320567; COSMIC: COSV54320567;