3-48626353-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022911.3(SLC26A6):c.2130C>A(p.Ser710Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,834 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022911.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A6 | NM_022911.3 | c.2130C>A | p.Ser710Arg | missense_variant, splice_region_variant | 20/21 | ENST00000395550.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A6 | ENST00000395550.7 | c.2130C>A | p.Ser710Arg | missense_variant, splice_region_variant | 20/21 | 1 | NM_022911.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248952Hom.: 1 AF XY: 0.000118 AC XY: 16AN XY: 135124
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461772Hom.: 1 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 727180
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.2130C>A (p.S710R) alteration is located in exon 20 (coding exon 20) of the SLC26A6 gene. This alteration results from a C to A substitution at nucleotide position 2130, causing the serine (S) at amino acid position 710 to be replaced by an arginine (R). 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