X-136024451-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001379110.1(SLC9A6):c.1428C>T(p.Gly476=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000179 in 111,423 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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 0.000018 ( 0 hom., 1 hem., cov: 23)
Consequence
SLC9A6
NM_001379110.1 synonymous
NM_001379110.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.524
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant X-136024451-C-T is Benign according to our data. Variant chrX-136024451-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 469634.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.524 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.1428C>T | p.Gly476= | synonymous_variant | 13/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.1428C>T | p.Gly476= | synonymous_variant | 13/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111423Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33619
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GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183373Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67851
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GnomAD4 exome Cov.: 30
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GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111423Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33619
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Christianson syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at