chrX-135985492-C-T

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

Scores

1
1

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.207
Variant links:
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
SLC9A6NM_001379110.1 linkuse as main transcriptc.-57+15C>T intron_variant ENST00000630721.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC9A6ENST00000630721.3 linkuse as main transcriptc.-57+15C>T intron_variant 4 NM_001379110.1

Frequencies

GnomAD3 genomes
AF:
0.000198
AC:
22
AN:
111032
Hom.:
0
Cov.:
22
AF XY:
0.000240
AC XY:
8
AN XY:
33370
show subpopulations
Gnomad AFR
AF:
0.000622
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000574
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000671
GnomAD3 exomes
AF:
0.0000809
AC:
3
AN:
37084
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
4844
show subpopulations
Gnomad AFR exome
AF:
0.000747
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000240
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000218
AC:
21
AN:
963400
Hom.:
0
Cov.:
27
AF XY:
0.0000201
AC XY:
6
AN XY:
298338
show subpopulations
Gnomad4 AFR exome
AF:
0.000614
Gnomad4 AMR exome
AF:
0.0000590
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000160
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000128
Gnomad4 OTH exome
AF:
0.0000491
GnomAD4 genome
AF:
0.000189
AC:
21
AN:
111073
Hom.:
0
Cov.:
22
AF XY:
0.000239
AC XY:
8
AN XY:
33421
show subpopulations
Gnomad4 AFR
AF:
0.000621
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000288
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000663
Alfa
AF:
0.0000454
Hom.:
0
Bravo
AF:
0.000189

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 submitterclinical testingGeneDxJun 30, 2017This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
14
DANN
Uncertain
0.98
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs781889579; hg19: chrX-135067651; API