11-26671139-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178498.4(SLC5A12):c.1820G>T(p.Ser607Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,474 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.1820G>T | p.Ser607Ile | missense_variant | Exon 15 of 15 | ENST00000396005.8 | NP_848593.2 | |
SLC5A12 | XM_006718155.4 | c.1487G>T | p.Ser496Ile | missense_variant | Exon 15 of 15 | XP_006718218.1 | ||
SLC5A12 | XM_011519920.3 | c.1256G>T | p.Ser419Ile | missense_variant | Exon 16 of 16 | XP_011518222.1 | ||
SLC5A12 | XM_017017244.2 | c.1256G>T | p.Ser419Ile | missense_variant | Exon 16 of 16 | XP_016872733.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A12 | ENST00000396005.8 | c.1820G>T | p.Ser607Ile | missense_variant | Exon 15 of 15 | 1 | NM_178498.4 | ENSP00000379326.3 | ||
SLC5A12 | ENST00000527405.5 | n.*426G>T | non_coding_transcript_exon_variant | Exon 15 of 15 | 2 | ENSP00000436011.1 | ||||
SLC5A12 | ENST00000527405.5 | n.*426G>T | 3_prime_UTR_variant | Exon 15 of 15 | 2 | ENSP00000436011.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460474Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726532
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1820G>T (p.S607I) alteration is located in exon 15 (coding exon 15) of the SLC5A12 gene. This alteration results from a G to T substitution at nucleotide position 1820, causing the serine (S) at amino acid position 607 to be replaced by an isoleucine (I). 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
Publications
No publications associated with this variant yet.