rs780281944
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_004172.5(SLC1A3):c.841C>T(p.Leu281=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,613,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
SLC1A3
NM_004172.5 synonymous
NM_004172.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.230
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 5-36677165-C-T is Benign according to our data. Variant chr5-36677165-C-T is described in ClinVar as [Benign]. Clinvar id is 586622.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.23 with no splicing effect.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC1A3 | NM_004172.5 | c.841C>T | p.Leu281= | synonymous_variant | 6/10 | ENST00000265113.9 | |
SLC1A3-AS1 | XR_007058736.1 | n.76-8454G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A3 | ENST00000265113.9 | c.841C>T | p.Leu281= | synonymous_variant | 6/10 | 1 | NM_004172.5 | P1 | |
SLC1A3-AS1 | ENST00000510740.1 | n.61-8454G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000517 AC: 130AN: 251296Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135828
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GnomAD4 exome AF: 0.000102 AC: 149AN: 1461378Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727062
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74362
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ClinVar
Significance: 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 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at