NM_004170.6:c.232+6775C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004170.6(SLC1A1):c.232+6775C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,272 control chromosomes in the GnomAD database, including 62,738 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 0.90 ( 62738 hom., cov: 32)
Consequence
SLC1A1
NM_004170.6 intron
NM_004170.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.663
Publications
2 publications found
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]
SLC1A1 Gene-Disease associations (from GenCC):
- dicarboxylic aminoaciduriaInheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
- hot water reflex epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.904 AC: 137517AN: 152154Hom.: 62707 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
137517
AN:
152154
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.904 AC: 137610AN: 152272Hom.: 62738 Cov.: 32 AF XY: 0.907 AC XY: 67549AN XY: 74456 show subpopulations
GnomAD4 genome
AF:
AC:
137610
AN:
152272
Hom.:
Cov.:
32
AF XY:
AC XY:
67549
AN XY:
74456
show subpopulations
African (AFR)
AF:
AC:
31922
AN:
41498
American (AMR)
AF:
AC:
14448
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
3421
AN:
3472
East Asian (EAS)
AF:
AC:
5117
AN:
5190
South Asian (SAS)
AF:
AC:
4763
AN:
4822
European-Finnish (FIN)
AF:
AC:
10150
AN:
10624
Middle Eastern (MID)
AF:
AC:
290
AN:
294
European-Non Finnish (NFE)
AF:
AC:
64665
AN:
68040
Other (OTH)
AF:
AC:
1941
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
618
1236
1853
2471
3089
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
900
1800
2700
3600
4500
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3382
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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