chr3-11017195-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003042.4(SLC6A1):c.-17C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,609,842 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0021 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 16 hom. )
Consequence
SLC6A1
NM_003042.4 5_prime_UTR
NM_003042.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.690
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=-0.74).
BP6
?
Variant 3-11017195-C-T is Benign according to our data. Variant chr3-11017195-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1217800.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00211 (322/152314) while in subpopulation NFE AF= 0.000661 (45/68032). AF 95% confidence interval is 0.000508. There are 7 homozygotes in gnomad4. There are 221 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 322 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.-17C>T | 5_prime_UTR_variant | 3/16 | ENST00000287766.10 | ||
SLC6A1-AS1 | NR_046647.1 | n.105+1925G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A1 | ENST00000287766.10 | c.-17C>T | 5_prime_UTR_variant | 3/16 | 1 | NM_003042.4 | P1 | ||
SLC6A1-AS1 | ENST00000414969.2 | n.105+1925G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00212 AC: 322AN: 152196Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00252 AC: 629AN: 249748Hom.: 11 AF XY: 0.00235 AC XY: 318AN XY: 135288
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GnomAD4 exome AF: 0.00113 AC: 1649AN: 1457528Hom.: 16 Cov.: 30 AF XY: 0.00110 AC XY: 794AN XY: 725060
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GnomAD4 genome ? AF: 0.00211 AC: 322AN: 152314Hom.: 7 Cov.: 32 AF XY: 0.00297 AC XY: 221AN XY: 74462
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | SLC6A1: PP2, BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 21, 2019 | - - |
Computational scores
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Name
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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