rs16927239
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004171.4(SLC1A2):c.1368C>T(p.Ala456=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,613,376 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00088 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 4 hom. )
Consequence
SLC1A2
NM_004171.4 synonymous
NM_004171.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.45
Genes affected
SLC1A2 (HGNC:10940): (solute carrier family 1 member 2) This gene encodes a member of a family of solute transporter proteins. The membrane-bound protein is the principal transporter that clears the excitatory neurotransmitter glutamate from the extracellular space at synapses in the central nervous system. Glutamate clearance is necessary for proper synaptic activation and to prevent neuronal damage from excessive activation of glutamate receptors. Improper regulation of this gene is thought to be associated with several neurological disorders. Alternatively spliced transcript variants of this gene have been identified. [provided by RefSeq, Jun 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 11-35280920-G-A is Benign according to our data. Variant chr11-35280920-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 767309.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-3.45 with no splicing effect.
BS2
?
High AC in GnomAd4 at 134 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC1A2 | NM_004171.4 | c.1368C>T | p.Ala456= | synonymous_variant | 9/11 | ENST00000278379.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A2 | ENST00000278379.9 | c.1368C>T | p.Ala456= | synonymous_variant | 9/11 | 1 | NM_004171.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000880 AC: 134AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00147 AC: 367AN: 250306Hom.: 2 AF XY: 0.00163 AC XY: 220AN XY: 135266
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GnomAD4 exome AF: 0.00152 AC: 2222AN: 1461052Hom.: 4 Cov.: 31 AF XY: 0.00164 AC XY: 1195AN XY: 726834
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GnomAD4 genome ? AF: 0.000880 AC: 134AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000886 AC XY: 66AN XY: 74490
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | SLC1A2: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at