rs386833477
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_000111.3(SLC26A3):c.332del(p.Phe111SerfsTer4) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000137 in 1,461,422 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. F111F) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000111.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A3 | NM_000111.3 | c.332del | p.Phe111SerfsTer4 | frameshift_variant | 4/21 | ENST00000340010.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A3 | ENST00000340010.10 | c.332del | p.Phe111SerfsTer4 | frameshift_variant | 4/21 | 1 | NM_000111.3 | P1 | |
SLC26A3 | ENST00000453332.1 | c.332del | p.Phe111SerfsTer4 | frameshift_variant | 4/4 | 4 | |||
SLC26A3 | ENST00000379083.7 | c.*123del | 3_prime_UTR_variant, NMD_transcript_variant | 4/20 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461422Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 727020
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Congenital secretory diarrhea, chloride type Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at