chr3-11015683-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003042.4(SLC6A1):c.-204G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,160 control chromosomes in the GnomAD database, including 17,991 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.47 ( 17973 hom., cov: 33)
Exomes 𝑓: 0.57 ( 18 hom. )
Consequence
SLC6A1
NM_003042.4 5_prime_UTR
NM_003042.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.451
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 3-11015683-G-A is Benign according to our data. Variant chr3-11015683-G-A is described in ClinVar as [Benign]. Clinvar id is 1246526.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.-204G>A | 5_prime_UTR_variant | 2/16 | ENST00000287766.10 | ||
SLC6A1-AS1 | NR_046647.1 | n.105+3437C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A1 | ENST00000287766.10 | c.-204G>A | 5_prime_UTR_variant | 2/16 | 1 | NM_003042.4 | P1 | ||
SLC6A1-AS1 | ENST00000414969.2 | n.105+3437C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.468 AC: 71136AN: 151920Hom.: 17960 Cov.: 33
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GnomAD4 exome AF: 0.566 AC: 69AN: 122Hom.: 18 Cov.: 0 AF XY: 0.598 AC XY: 49AN XY: 82
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GnomAD4 genome AF: 0.468 AC: 71177AN: 152038Hom.: 17973 Cov.: 33 AF XY: 0.469 AC XY: 34828AN XY: 74314
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 19, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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