17-82237378-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004207.4(SLC16A3):c.608C>T(p.Thr203Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,541,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004207.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC16A3 | NM_004207.4 | c.608C>T | p.Thr203Met | missense_variant | 4/5 | ENST00000582743.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC16A3 | ENST00000582743.6 | c.608C>T | p.Thr203Met | missense_variant | 4/5 | 1 | NM_004207.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000100 AC: 15AN: 149910Hom.: 0 AF XY: 0.000110 AC XY: 9AN XY: 81854
GnomAD4 exome AF: 0.0000403 AC: 56AN: 1388860Hom.: 0 Cov.: 31 AF XY: 0.0000351 AC XY: 24AN XY: 683862
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.608C>T (p.T203M) alteration is located in exon 4 (coding exon 3) of the SLC16A3 gene. This alteration results from a C to T substitution at nucleotide position 608, causing the threonine (T) at amino acid position 203 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at