chrX-135985492-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000370695.8(SLC9A6):c.-11C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,074,473 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 0.00019 ( 0 hom., 8 hem., cov: 22)
Exomes 𝑓: 0.000022 ( 0 hom. 6 hem. )
Consequence
SLC9A6
ENST00000370695.8 5_prime_UTR
ENST00000370695.8 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.207
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant X-135985492-C-T is Benign according to our data. Variant chrX-135985492-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 516672.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 8 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.-57+15C>T | intron_variant | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.-57+15C>T | intron_variant | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes AF: 0.000198 AC: 22AN: 111032Hom.: 0 Cov.: 22 AF XY: 0.000240 AC XY: 8AN XY: 33370
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GnomAD3 exomes AF: 0.0000809 AC: 3AN: 37084Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 4844
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GnomAD4 exome AF: 0.0000218 AC: 21AN: 963400Hom.: 0 Cov.: 27 AF XY: 0.0000201 AC XY: 6AN XY: 298338
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GnomAD4 genome AF: 0.000189 AC: 21AN: 111073Hom.: 0 Cov.: 22 AF XY: 0.000239 AC XY: 8AN XY: 33421
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2017 | 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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
RBP_binding_hub_radar
RBP_regulation_power_radar
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