22-32110117-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000343.4(SLC5A1):c.1899G>T(p.Thr633=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,818 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. Synonymous variant affecting the same amino acid position (i.e. T633T) has been classified as Benign.
Frequency
Consequence
NM_000343.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A1 | NM_000343.4 | c.1899G>T | p.Thr633= | synonymous_variant | 15/15 | ENST00000266088.9 | |
LOC105373000 | XR_938172.3 | n.408-3175C>A | intron_variant, non_coding_transcript_variant | ||||
SLC5A1 | NM_001256314.2 | c.1518G>T | p.Thr506= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A1 | ENST00000266088.9 | c.1899G>T | p.Thr633= | synonymous_variant | 15/15 | 1 | NM_000343.4 | P1 | |
SLC5A1 | ENST00000543737.2 | c.1518G>T | p.Thr506= | synonymous_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461818Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727210
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at