1-205921736-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052934.4(SLC26A9):c.1885C>T(p.Pro629Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000044 in 1,592,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
SLC26A9
NM_052934.4 missense
NM_052934.4 missense
Scores
7
10
Clinical Significance
Conservation
PhyloP100: 4.97
Genes affected
SLC26A9 (HGNC:14469): (solute carrier family 26 member 9) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.15374306).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A9 | NM_052934.4 | c.1885C>T | p.Pro629Ser | missense_variant | 17/21 | ENST00000367135.8 | |
SLC26A9 | NM_134325.3 | c.1885C>T | p.Pro629Ser | missense_variant | 17/22 | ||
SLC26A9 | XM_011509121.3 | c.1618C>T | p.Pro540Ser | missense_variant | 16/20 | ||
SLC26A9 | XM_011509122.3 | c.1393C>T | p.Pro465Ser | missense_variant | 14/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A9 | ENST00000367135.8 | c.1885C>T | p.Pro629Ser | missense_variant | 17/21 | 1 | NM_052934.4 | P1 | |
SLC26A9 | ENST00000340781.8 | c.1885C>T | p.Pro629Ser | missense_variant | 16/21 | 1 | |||
SLC26A9 | ENST00000367134.2 | c.1885C>T | p.Pro629Ser | missense_variant | 17/22 | 5 | |||
SLC26A9 | ENST00000491127.5 | n.1269C>T | non_coding_transcript_exon_variant | 9/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000208 AC: 3AN: 1440018Hom.: 0 Cov.: 35 AF XY: 0.00000140 AC XY: 1AN XY: 714256
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2022 | The c.1885C>T (p.P629S) alteration is located in exon 17 (coding exon 16) of the SLC26A9 gene. This alteration results from a C to T substitution at nucleotide position 1885, causing the proline (P) at amino acid position 629 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.10
.;B;.
Vest4
MutPred
Gain of phosphorylation at P629 (P = 0.0101);Gain of phosphorylation at P629 (P = 0.0101);Gain of phosphorylation at P629 (P = 0.0101);
MVP
MPC
0.17
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at