Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003042.4(SLC6A1):c.-93G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000012 in 835,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
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]
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
21546
American (AMR)
AF:
0.00
AC:
0
AN:
38948
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19042
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35300
South Asian (SAS)
AF:
0.0000158
AC:
1
AN:
63210
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47452
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3044
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
567234
Other (OTH)
AF:
0.00
AC:
0
AN:
39256
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.