rs869312806
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_004174.4(SLC9A3):c.932C>T(p.Ala311Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,510 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A311T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004174.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.932C>T | p.Ala311Val | missense_variant, splice_region_variant | 5/17 | ENST00000264938.8 | |
SLC9A3 | NM_001284351.3 | c.932C>T | p.Ala311Val | missense_variant, splice_region_variant | 5/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.932C>T | p.Ala311Val | missense_variant, splice_region_variant | 5/17 | 1 | NM_004174.4 | P2 | |
SLC9A3 | ENST00000514375.1 | c.932C>T | p.Ala311Val | missense_variant, splice_region_variant | 5/17 | 1 | |||
SLC9A3 | ENST00000644203.1 | c.932C>T | p.Ala311Val | missense_variant, splice_region_variant | 5/16 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460510Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726598
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Congenital secretory sodium diarrhea 8 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at