rs782529317
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001379110.1(SLC9A6):c.228T>C(p.Asn76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,666 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000036 ( 0 hom. 13 hem. )
Consequence
SLC9A6
NM_001379110.1 synonymous
NM_001379110.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0950
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=-0.56).
BP6
?
Variant X-135994844-T-C is Benign according to our data. Variant chrX-135994844-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 415902.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.095 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.228T>C | p.Asn76= | synonymous_variant | 3/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.228T>C | p.Asn76= | synonymous_variant | 3/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000537 AC: 6AN: 111732Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33900
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GnomAD3 exomes AF: 0.0000599 AC: 11AN: 183515Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67943
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GnomAD4 exome AF: 0.0000355 AC: 39AN: 1097934Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 13AN XY: 363298
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GnomAD4 genome ? AF: 0.0000537 AC: 6AN: 111732Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33900
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2017 | This alteration is classified as likely 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Christianson syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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