chrX-136044736-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001379110.1(SLC9A6):c.*12C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,204,813 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., 4 hem., cov: 22)
Exomes 𝑓: 0.000032 ( 0 hom. 13 hem. )
Consequence
SLC9A6
NM_001379110.1 3_prime_UTR
NM_001379110.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0580
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant X-136044736-C-T is Benign according to our data. Variant chrX-136044736-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 212217.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
?
High Hemizygotes in GnomAd at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.*12C>T | 3_prime_UTR_variant | 18/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.*12C>T | 3_prime_UTR_variant | 18/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000107 AC: 12AN: 112103Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34267
GnomAD3 genomes
?
AF:
AC:
12
AN:
112103
Hom.:
Cov.:
22
AF XY:
AC XY:
4
AN XY:
34267
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183000Hom.: 0 AF XY: 0.0000592 AC XY: 4AN XY: 67574
GnomAD3 exomes
AF:
AC:
10
AN:
183000
Hom.:
AF XY:
AC XY:
4
AN XY:
67574
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000320 AC: 35AN: 1092655Hom.: 0 Cov.: 29 AF XY: 0.0000363 AC XY: 13AN XY: 358267
GnomAD4 exome
AF:
AC:
35
AN:
1092655
Hom.:
Cov.:
29
AF XY:
AC XY:
13
AN XY:
358267
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000107 AC: 12AN: 112158Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34332
GnomAD4 genome
?
AF:
AC:
12
AN:
112158
Hom.:
Cov.:
22
AF XY:
AC XY:
4
AN XY:
34332
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2016 | 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at