rs930072

Positions:

• chr5-36665969-C-T

Variant summary

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

The NM_004172.5(SLC1A3):​c.320-5060C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,170 control chromosomes in the GnomAD database, including 38,415 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 0.64 (38415 hom., cov: 33)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A3	NM_004172.5	c.320-5060C>T		intron_variant		ENST00000265113.9
SLC1A3-AS1	XR_007058736.1	n.2818G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A3	ENST00000265113.9	c.320-5060C>T		intron_variant		1	NM_004172.5	P1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97831 AN: 152052 Hom.: 38428 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.643 AC: 97823 AN: 152170 Hom.: 38415 Cov.: 33 AF XY: 0.642 AC XY: 47789 AN XY: 74420

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.676

Alfa AF: 0.833 Hom.: 115283

Bravo AF: 0.609

Asia WGS AF: 0.514 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.78

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: rs930072; hg19: chr5-36666071;