11-26673490-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178498.4(SLC5A12):c.1619G>A(p.Arg540Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,611,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178498.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A12 | NM_178498.4 | c.1619G>A | p.Arg540Lys | missense_variant | Exon 14 of 15 | ENST00000396005.8 | NP_848593.2 | |
SLC5A12 | XM_006718155.4 | c.1286G>A | p.Arg429Lys | missense_variant | Exon 14 of 15 | XP_006718218.1 | ||
SLC5A12 | XM_011519920.3 | c.1055G>A | p.Arg352Lys | missense_variant | Exon 15 of 16 | XP_011518222.1 | ||
SLC5A12 | XM_017017244.2 | c.1055G>A | p.Arg352Lys | missense_variant | Exon 15 of 16 | XP_016872733.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A12 | ENST00000396005.8 | c.1619G>A | p.Arg540Lys | missense_variant | Exon 14 of 15 | 1 | NM_178498.4 | ENSP00000379326.3 | ||
SLC5A12 | ENST00000527405.5 | n.*225G>A | non_coding_transcript_exon_variant | Exon 14 of 15 | 2 | ENSP00000436011.1 | ||||
SLC5A12 | ENST00000527405.5 | n.*225G>A | 3_prime_UTR_variant | Exon 14 of 15 | 2 | ENSP00000436011.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000284 AC: 7AN: 246704Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133878
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459456Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 725930
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1619G>A (p.R540K) alteration is located in exon 14 (coding exon 14) of the SLC5A12 gene. This alteration results from a G to A substitution at nucleotide position 1619, causing the arginine (R) at amino acid position 540 to be replaced by a lysine (K). 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