rs1060502675
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001379110.1(SLC9A6):āc.206A>Gā(p.His69Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,098,073 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 23)
Exomes š: 9.1e-7 ( 0 hom. 0 hem. )
Consequence
SLC9A6
NM_001379110.1 missense
NM_001379110.1 missense
Scores
1
4
5
Clinical Significance
Conservation
PhyloP100: 4.65
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant X-135994822-A-G is Benign according to our data. Variant chrX-135994822-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 409978.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.206A>G | p.His69Arg | missense_variant | 3/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.206A>G | p.His69Arg | missense_variant | 3/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098073Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 363437
GnomAD4 exome
AF:
AC:
1
AN:
1098073
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
363437
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
Bravo
AF:
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 | Feb 05, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
Polyphen
0.0040, 0.0010
.;.;.;.;.;.;B;B;.;.
Vest4
0.43, 0.46, 0.49
MutPred
0.58
.;.;.;.;.;.;Gain of solvent accessibility (P = 0.0171);Gain of solvent accessibility (P = 0.0171);.;.;
MVP
0.93
MPC
1.7
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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