3-11016978-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003042.4(SLC6A1):c.-153-81C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00841 in 539,788 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 49 hom., cov: 32)
Exomes 𝑓: 0.0054 ( 41 hom. )
Consequence
SLC6A1
NM_003042.4 intron
NM_003042.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.649
Publications
1 publications found
Genes affected
SLC6A1 (HGNC:11042): (solute carrier family 6 member 1) The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 3-11016978-C-T is Benign according to our data. Variant chr3-11016978-C-T is described in ClinVar as [Benign]. Clinvar id is 1226679.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0161 (2447/152182) while in subpopulation AFR AF = 0.0503 (2089/41498). AF 95% confidence interval is 0.0485. There are 49 homozygotes in GnomAd4. There are 1213 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 2447 AD,Unknown gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.-153-81C>T | intron_variant | Intron 2 of 15 | ENST00000287766.10 | NP_003033.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2445AN: 152064Hom.: 48 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2445
AN:
152064
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:
GnomAD4 exome AF: 0.00540 AC: 2095AN: 387606Hom.: 41 AF XY: 0.00607 AC XY: 1230AN XY: 202652 show subpopulations
GnomAD4 exome
AF:
AC:
2095
AN:
387606
Hom.:
AF XY:
AC XY:
1230
AN XY:
202652
show subpopulations
African (AFR)
AF:
AC:
564
AN:
11194
American (AMR)
AF:
AC:
59
AN:
15582
Ashkenazi Jewish (ASJ)
AF:
AC:
55
AN:
12228
East Asian (EAS)
AF:
AC:
270
AN:
26418
South Asian (SAS)
AF:
AC:
907
AN:
40270
European-Finnish (FIN)
AF:
AC:
2
AN:
24636
Middle Eastern (MID)
AF:
AC:
10
AN:
1718
European-Non Finnish (NFE)
AF:
AC:
72
AN:
232798
Other (OTH)
AF:
AC:
156
AN:
22762
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
100
200
301
401
501
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0161 AC: 2447AN: 152182Hom.: 49 Cov.: 32 AF XY: 0.0163 AC XY: 1213AN XY: 74394 show subpopulations
GnomAD4 genome
AF:
AC:
2447
AN:
152182
Hom.:
Cov.:
32
AF XY:
AC XY:
1213
AN XY:
74394
show subpopulations
African (AFR)
AF:
AC:
2089
AN:
41498
American (AMR)
AF:
AC:
105
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
16
AN:
3472
East Asian (EAS)
AF:
AC:
49
AN:
5178
South Asian (SAS)
AF:
AC:
123
AN:
4804
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
32
AN:
68012
Other (OTH)
AF:
AC:
30
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
112
224
335
447
559
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
112
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Jul 26, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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