1-205915163-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000340781.8(SLC26A9):c.2393G>A(p.Gly798Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,460,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000340781.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A9 | NM_052934.4 | c.*194G>A | 3_prime_UTR_variant | 21/21 | ENST00000367135.8 | ||
SLC26A9 | NM_134325.3 | c.2393G>A | p.Gly798Glu | missense_variant | 22/22 | ||
SLC26A9 | XM_011509121.3 | c.*194G>A | 3_prime_UTR_variant | 20/20 | |||
SLC26A9 | XM_011509122.3 | c.*194G>A | 3_prime_UTR_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A9 | ENST00000340781.8 | c.2393G>A | p.Gly798Glu | missense_variant | 21/21 | 1 | |||
SLC26A9 | ENST00000367135.8 | c.*194G>A | 3_prime_UTR_variant | 21/21 | 1 | NM_052934.4 | P1 | ||
SLC26A9 | ENST00000367134.2 | c.2393G>A | p.Gly798Glu | missense_variant | 22/22 | 5 | |||
SLC26A9 | ENST00000491127.5 | n.1954G>A | non_coding_transcript_exon_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249636Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134930
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460436Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726246
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.2393G>A (p.G798E) alteration is located in exon 22 (coding exon 21) of the SLC26A9 gene. This alteration results from a G to A substitution at nucleotide position 2393, causing the glycine (G) at amino acid position 798 to be replaced by a glutamic acid (E). 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