rs13173144

Variant names:

• chr5-36608922-T-A
• rs13173144
• ENST00000512374.1:c.*301T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-36608922-T-A
• chr5-36608922-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001166696.3(SLC1A3):​c.*301T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC1A3 NM_001166696.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 3 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 Gene-Disease associations (from GenCC):

• episodic ataxia type 6

  Inheritance: Unknown, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Laboratory for Molecular Medicine, Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166696.3. 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.181+318T>A		intron	N/A	NP_004163.3
	SLC1A3	NM_001166696.3		c.*301T>A		3_prime_UTR	Exon 2 of 2	NP_001160168.1	Q7Z5T0
	SLC1A3	NM_001438458.1		c.181+318T>A		intron	N/A	NP_001425387.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A3	ENST00000512374.1	TSL:1	c.*301T>A		3_prime_UTR	Exon 2 of 2	ENSP00000506048.1	Q7Z5T0
	SLC1A3	ENST00000265113.9	TSL:1 MANE Select	c.181+318T>A		intron	N/A	ENSP00000265113.4	P43003-1
	SLC1A3	ENST00000381918.4	TSL:1	c.181+318T>A		intron	N/A	ENSP00000371343.4	P43003-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 908914 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 423216

African (AFR) AF: 0.00 AC: 0 AN: 18306

American (AMR) AF: 0.00 AC: 0 AN: 5006

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8058

East Asian (EAS) AF: 0.00 AC: 0 AN: 9150

South Asian (SAS) AF: 0.00 AC: 0 AN: 20734

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3490

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1958

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 810000

Other (OTH) AF: 0.00 AC: 0 AN: 32212

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-2.0

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: rs13173144; hg19: chr5-36609024;