chrX-153688592-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005629.4(SLC6A8):c.18C>G(p.Ala6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000422 in 947,071 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A6A) has been classified as Likely benign.
Frequency
Consequence
NM_005629.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.18C>G | p.Ala6= | synonymous_variant | 1/13 | ENST00000253122.10 | |
SLC6A8 | NM_001142805.2 | c.18C>G | p.Ala6= | synonymous_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.18C>G | p.Ala6= | synonymous_variant | 1/13 | 1 | NM_005629.4 | P1 | |
PNCK | ENST00000458354.5 | c.-3+223G>C | intron_variant | 3 | |||||
PNCK | ENST00000480693.1 | n.64+223G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD4 exome AF: 0.00000422 AC: 4AN: 947071Hom.: 0 Cov.: 24 AF XY: 0.00000332 AC XY: 1AN XY: 300969
GnomAD4 genome ? Cov.: 20
ClinVar
Submissions by phenotype
Creatine transporter deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at