chrX-135985154-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000370701.6(SLC9A6):c.-380C>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 0.0165 in 175,759 control chromosomes in the GnomAD database, including 33 homozygotes. There are 772 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 0.015 ( 16 hom., 436 hem., cov: 22)
Exomes 𝑓: 0.020 ( 17 hom. 336 hem. )
Consequence
SLC9A6
ENST00000370701.6 5_prime_UTR
ENST00000370701.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant X-135985154-C-T is Benign according to our data. Variant chrX-135985154-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 669883.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (1643/111493) while in subpopulation NFE AF= 0.0237 (1258/52996). AF 95% confidence interval is 0.0226. There are 16 homozygotes in gnomad4. There are 436 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 16 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001400909.1 | c.-35-470C>T | intron_variant | ||||
SLC9A6 | NM_001400910.1 | c.-56-449C>T | intron_variant | ||||
SLC9A6 | NM_001400911.1 | c.-56-449C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000370701.6 | c.-380C>T | 5_prime_UTR_variant | 1/17 | 1 | A1 | |||
SLC9A6 | ENST00000636092.1 | c.-56-449C>T | intron_variant | 5 | A1 | ||||
SLC9A6 | ENST00000636347.1 | c.-35-470C>T | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 1644AN: 111454Hom.: 16 Cov.: 22 AF XY: 0.0130 AC XY: 437AN XY: 33630
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GnomAD4 exome AF: 0.0197 AC: 1264AN: 64266Hom.: 17 Cov.: 0 AF XY: 0.0211 AC XY: 336AN XY: 15888
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GnomAD4 genome AF: 0.0147 AC: 1643AN: 111493Hom.: 16 Cov.: 22 AF XY: 0.0129 AC XY: 436AN XY: 33679
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | 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
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at