chr7-107791855-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000111.3(SLC26A3):c.357C>A(p.Phe119Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,612,342 control chromosomes in the GnomAD database, including 147 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. F119F) has been classified as Benign.
Frequency
Consequence
NM_000111.3 missense
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>A | p.Phe119Leu | missense_variant | Exon 4 of 21 | 1 | NM_000111.3 | ENSP00000345873.5 | ||
SLC26A3 | ENST00000453332.1 | c.357C>A | p.Phe119Leu | missense_variant | Exon 4 of 4 | 4 | ENSP00000395955.1 | |||
SLC26A3 | ENST00000379083.7 | n.*148C>A | non_coding_transcript_exon_variant | Exon 4 of 20 | 2 | ENSP00000368375.3 | ||||
SLC26A3 | ENST00000379083.7 | n.*148C>A | 3_prime_UTR_variant | Exon 4 of 20 | 2 | ENSP00000368375.3 |
Frequencies
GnomAD3 genomes AF: 0.00875 AC: 1330AN: 152074Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.00867 AC: 2179AN: 251348Hom.: 12 AF XY: 0.00866 AC XY: 1177AN XY: 135834
GnomAD4 exome AF: 0.0116 AC: 16870AN: 1460150Hom.: 128 Cov.: 29 AF XY: 0.0111 AC XY: 8069AN XY: 726474
GnomAD4 genome AF: 0.00873 AC: 1329AN: 152192Hom.: 19 Cov.: 32 AF XY: 0.00883 AC XY: 657AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:4
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This variant is associated with the following publications: (PMID: 29079751) -
Congenital secretory diarrhea, chloride type Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at