22-38080849-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_013356.3(SLC16A8):c.1189C>T(p.Pro397Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000264 in 1,514,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC16A8 | NM_013356.3 | c.1189C>T | p.Pro397Ser | missense_variant | Exon 5 of 6 | ENST00000681075.2 | NP_037488.2 | |
SLC16A8 | XM_017028685.2 | c.1189C>T | p.Pro397Ser | missense_variant | Exon 3 of 4 | XP_016884174.1 | ||
SLC16A8 | NM_001394131.1 | c.-80-2145C>T | intron_variant | Intron 1 of 1 | NP_001381060.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC16A8 | ENST00000681075.2 | c.1189C>T | p.Pro397Ser | missense_variant | Exon 5 of 6 | NM_013356.3 | ENSP00000506669.1 | |||
SLC16A8 | ENST00000320521.10 | c.1189C>T | p.Pro397Ser | missense_variant | Exon 4 of 5 | 1 | ENSP00000321735.5 | |||
SLC16A8 | ENST00000469516.5 | n.107-2145C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000172 AC: 2AN: 116086Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63672
GnomAD4 exome AF: 0.00000220 AC: 3AN: 1362070Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 670756
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1189C>T (p.P397S) alteration is located in exon 4 (coding exon 3) of the SLC16A8 gene. This alteration results from a C to T substitution at nucleotide position 1189, causing the proline (P) at amino acid position 397 to be replaced by a serine (S). 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