rs376421364
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005629.4(SLC6A8):āc.1452C>Gā(p.Leu484=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,208,822 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 50 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L484L) has been classified as Likely benign.
Frequency
Consequence
NM_005629.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1452C>G | p.Leu484= | synonymous_variant | 10/13 | ENST00000253122.10 | |
SLC6A8 | NM_001142805.2 | c.1422C>G | p.Leu474= | synonymous_variant | 10/13 | ||
SLC6A8 | NM_001142806.1 | c.1107C>G | p.Leu369= | synonymous_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1452C>G | p.Leu484= | synonymous_variant | 10/13 | 1 | NM_005629.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000807 AC: 9AN: 111551Hom.: 0 Cov.: 23 AF XY: 0.0000593 AC XY: 2AN XY: 33727
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 182849Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67703
GnomAD4 exome AF: 0.000137 AC: 150AN: 1097271Hom.: 0 Cov.: 34 AF XY: 0.000132 AC XY: 48AN XY: 362753
GnomAD4 genome ? AF: 0.0000807 AC: 9AN: 111551Hom.: 0 Cov.: 23 AF XY: 0.0000593 AC XY: 2AN XY: 33727
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | SLC6A8: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 08, 2021 | - - |
Creatine transporter deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 18, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at