rs142049079
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001379110.1(SLC9A6):c.1029A>C(p.Ala343=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,206,366 control chromosomes in the GnomAD database, including 22 homozygotes. There are 2,039 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0041 ( 2 hom., 120 hem., cov: 24)
Exomes 𝑓: 0.0052 ( 20 hom. 1919 hem. )
Consequence
SLC9A6
NM_001379110.1 synonymous
NM_001379110.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.409
Genes affected
SLC9A6 (HGNC:11079): (solute carrier family 9 member A6) This gene encodes a sodium-hydrogen exchanger that is amember of the solute carrier family 9. The encoded protein localizes to early and recycling endosomes and may be involved in regulating endosomal pH and volume. Defects in this gene are associated with X-linked syndromic cognitive disability, Christianson type. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant X-136013386-A-C is Benign according to our data. Variant chrX-136013386-A-C is described in ClinVar as [Benign]. Clinvar id is 139203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-136013386-A-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.409 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.1029A>C | p.Ala343= | synonymous_variant | 10/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.1029A>C | p.Ala343= | synonymous_variant | 10/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00407 AC: 456AN: 111963Hom.: 2 Cov.: 24 AF XY: 0.00352 AC XY: 120AN XY: 34123
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GnomAD3 exomes AF: 0.00463 AC: 849AN: 183404Hom.: 2 AF XY: 0.00532 AC XY: 361AN XY: 67868
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GnomAD4 exome AF: 0.00515 AC: 5639AN: 1094351Hom.: 20 Cov.: 29 AF XY: 0.00533 AC XY: 1919AN XY: 359893
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GnomAD4 genome ? AF: 0.00407 AC: 456AN: 112015Hom.: 2 Cov.: 24 AF XY: 0.00351 AC XY: 120AN XY: 34185
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 12, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 15, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2012 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 30, 2016 | - - |
Christianson syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 03, 2021 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 25, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at