chr2-27201042-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021095.4(SLC5A6):c.1720C>T(p.Pro574Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P574P) has been classified as Benign.
Frequency
Consequence
NM_021095.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A6 | NM_021095.4 | c.1720C>T | p.Pro574Ser | missense_variant | 16/17 | ENST00000310574.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A6 | ENST00000310574.8 | c.1720C>T | p.Pro574Ser | missense_variant | 16/17 | 1 | NM_021095.4 | P1 | |
SLC5A6 | ENST00000408041.5 | c.1720C>T | p.Pro574Ser | missense_variant | 17/18 | 1 | P1 | ||
SLC5A6 | ENST00000461757.1 | n.1270C>T | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
SLC5A6 | ENST00000488743.6 | n.2406C>T | non_coding_transcript_exon_variant | 15/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152140Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251232Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135764
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461678Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727148
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74430
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.1720C>T (p.P574S) alteration is located in exon 16 (coding exon 14) of the SLC5A6 gene. This alteration results from a C to T substitution at nucleotide position 1720, causing the proline (P) at amino acid position 574 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