rs73419912
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000111.3(SLC26A3):c.357C>T(p.Phe119Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,612,592 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000111.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A3 | ENST00000340010.10 | c.357C>T | p.Phe119Phe | synonymous_variant | Exon 4 of 21 | 1 | NM_000111.3 | ENSP00000345873.5 | ||
SLC26A3 | ENST00000453332.1 | c.357C>T | p.Phe119Phe | synonymous_variant | Exon 4 of 4 | 4 | ENSP00000395955.1 | |||
SLC26A3 | ENST00000379083.7 | n.*148C>T | non_coding_transcript_exon_variant | Exon 4 of 20 | 2 | ENSP00000368375.3 | ||||
SLC26A3 | ENST00000379083.7 | n.*148C>T | 3_prime_UTR_variant | Exon 4 of 20 | 2 | ENSP00000368375.3 |
Frequencies
GnomAD3 genomes AF: 0.00437 AC: 665AN: 152070Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00171 AC: 431AN: 251348Hom.: 2 AF XY: 0.00148 AC XY: 201AN XY: 135834
GnomAD4 exome AF: 0.00148 AC: 2157AN: 1460404Hom.: 5 Cov.: 29 AF XY: 0.00138 AC XY: 1005AN XY: 726596
GnomAD4 genome AF: 0.00437 AC: 665AN: 152188Hom.: 4 Cov.: 32 AF XY: 0.00411 AC XY: 306AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:3
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SLC26A3: BS1, BS2 -
Congenital secretory diarrhea, chloride type Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at