rs3776572

chr5-36645930-C-Gchr5-36645930-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.319+16343C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,082 control chromosomes in the GnomAD database, including 27,949 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 0.59 (27949 hom., cov: 32)
• Consequence: SLC1A3 NM_004172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A3	NM_004172.5	c.319+16343C>G		intron_variant		ENST00000265113.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A3	ENST00000265113.9	c.319+16343C>G		intron_variant		1	NM_004172.5	P1
	ENST00000618632.1	n.33+3385G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89582 AN: 151964 Hom.: 27954 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.589 AC: 89591 AN: 152082 Hom.: 27949 Cov.: 32 AF XY: 0.593 AC XY: 44093 AN XY: 74334

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.615

Alfa AF: 0.640 Hom.: 4008

Bravo AF: 0.575

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.80

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: rs3776572; hg19: chr5-36646032;