chr22-32229236-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014227.3(SLC5A4):c.1238T>C(p.Met413Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014227.3 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 |
---|---|---|---|---|---|---|---|
SLC5A4 | NM_014227.3 | c.1238T>C | p.Met413Thr | missense_variant | 11/15 | ENST00000266086.6 | |
SLC5A4-AS1 | NR_149072.1 | n.274+21960A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A4 | ENST00000266086.6 | c.1238T>C | p.Met413Thr | missense_variant | 11/15 | 1 | NM_014227.3 | P1 | |
SLC5A4-AS1 | ENST00000452181.2 | n.274+21960A>G | intron_variant, non_coding_transcript_variant | 5 | |||||
SLC5A4-AS1 | ENST00000434942.2 | n.371A>G | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251354Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135836
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727222
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.1238T>C (p.M413T) alteration is located in exon 11 (coding exon 11) of the SLC5A4 gene. This alteration results from a T to C substitution at nucleotide position 1238, causing the methionine (M) at amino acid position 413 to be replaced by a threonine (T). 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