rs144252036
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The ENST00000253122.10(SLC6A8):c.1020C>T(p.Asp340=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000736 in 1,209,311 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000253122.10 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1020C>T | p.Asp340= | synonymous_variant | 7/13 | ENST00000253122.10 | NP_005620.1 | |
SLC6A8 | NM_001142806.1 | c.675C>T | p.Asp225= | synonymous_variant | 7/13 | NP_001136278.1 | ||
SLC6A8 | NM_001142805.2 | c.1017-27C>T | intron_variant | NP_001136277.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1020C>T | p.Asp340= | synonymous_variant | 7/13 | 1 | NM_005629.4 | ENSP00000253122 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 25AN: 111684Hom.: 0 Cov.: 24 AF XY: 0.000118 AC XY: 4AN XY: 33852
GnomAD3 exomes AF: 0.000125 AC: 23AN: 183363Hom.: 0 AF XY: 0.0000884 AC XY: 6AN XY: 67881
GnomAD4 exome AF: 0.0000583 AC: 64AN: 1097577Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 17AN XY: 362975
GnomAD4 genome AF: 0.000224 AC: 25AN: 111734Hom.: 0 Cov.: 24 AF XY: 0.000118 AC XY: 4AN XY: 33912
ClinVar
Submissions by phenotype
Creatine transporter deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 25, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at