NM_004172.5:c.320-5060C>T

Variant names:

• chr5-36665969-C-T
• rs930072
• NM_004172.5:c.320-5060C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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:56374): (SLC1A3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004172.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A3	NM_004172.5	MANE Select	c.320-5060C>T		intron	N/A	NP_004163.3
	SLC1A3	NM_001438458.1		c.320-5060C>T		intron	N/A	NP_001425387.1
	SLC1A3	NM_001438454.1		c.320-5060C>T		intron	N/A	NP_001425383.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A3	ENST00000265113.9	TSL:1 MANE Select	c.320-5060C>T		intron	N/A	ENSP00000265113.4	P43003-1
	SLC1A3	ENST00000381918.4	TSL:1	c.320-5060C>T		intron	N/A	ENSP00000371343.4	P43003-1
	SLC1A3	ENST00000680232.1		c.320-5060C>T		intron	N/A	ENSP00000506207.1	A0A7P0TAG7

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

African (AFR) AF: 0.186 AC: 7717 AN: 41488

American (AMR) AF: 0.689 AC: 10528 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1948 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3435 AN: 4816

European-Finnish (FIN) AF: 0.866 AC: 9188 AN: 10608

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59697 AN: 68018

Other (OTH) AF: 0.676 AC: 1426 AN: 2108

Alfa AF: 0.787 Hom.: 152846

Bravo AF: 0.609

Asia WGS AF: 0.514 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		-0.38
Mutation Taster		=96/4	polymorphism (auto)

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

Other links and lift over

dbSNP: rs930072; hg19: chr5-36666071;