chr9-4561596-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004170.6(SLC1A1):c.325+55G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,130,482 control chromosomes in the GnomAD database, including 40,238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5051 hom., cov: 32)
Exomes 𝑓: 0.26 ( 35187 hom. )
Consequence
SLC1A1
NM_004170.6 intron
NM_004170.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.419
Genes affected
SLC1A1 (HGNC:10939): (solute carrier family 1 member 1) This gene encodes a member of the high-affinity glutamate transporters that play an essential role in transporting glutamate across plasma membranes. In brain, these transporters are crucial in terminating the postsynaptic action of the neurotransmitter glutamate, and in maintaining extracellular glutamate concentrations below neurotoxic levels. This transporter also transports aspartate, and mutations in this gene are thought to cause dicarboxylicamino aciduria, also known as glutamate-aspartate transport defect. [provided by RefSeq, Mar 2010]
SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 9-4561596-G-A is Benign according to our data. Variant chr9-4561596-G-A is described in ClinVar as [Benign]. Clinvar id is 1239990.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC1A1 | NM_004170.6 | c.325+55G>A | intron_variant | ENST00000262352.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC1A1 | ENST00000262352.8 | c.325+55G>A | intron_variant | 1 | NM_004170.6 | P1 | |||
SPATA6L | ENST00000485616.5 | c.*782-7208C>T | intron_variant, NMD_transcript_variant | 2 | |||||
SLC1A1 | ENST00000490167.1 | n.369+55G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.247 AC: 37427AN: 151774Hom.: 5047 Cov.: 32
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GnomAD4 exome AF: 0.259 AC: 253504AN: 978588Hom.: 35187 AF XY: 0.254 AC XY: 129028AN XY: 508368
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GnomAD4 genome ? AF: 0.247 AC: 37443AN: 151894Hom.: 5051 Cov.: 32 AF XY: 0.252 AC XY: 18714AN XY: 74242
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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