chrX-135998934-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001379110.1(SLC9A6):āc.603A>Gā(p.Leu201Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,089,953 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 23)
Exomes š: 0.000015 ( 0 hom. 6 hem. )
Consequence
SLC9A6
NM_001379110.1 synonymous
NM_001379110.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00500
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant X-135998934-A-G is Benign according to our data. Variant chrX-135998934-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 415900.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.005 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.603A>G | p.Leu201Leu | synonymous_variant | 6/18 | ENST00000630721.3 | NP_001366039.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.603A>G | p.Leu201Leu | synonymous_variant | 6/18 | 4 | NM_001379110.1 | ENSP00000487486.2 | ||
SLC9A6 | ENST00000370695.8 | c.759A>G | p.Leu253Leu | synonymous_variant | 5/16 | 1 | ENSP00000359729.4 | |||
SLC9A6 | ENST00000370698.7 | c.663A>G | p.Leu221Leu | synonymous_variant | 5/16 | 1 | ENSP00000359732.3 | |||
SLC9A6 | ENST00000370701.6 | c.603A>G | p.Leu201Leu | synonymous_variant | 6/17 | 1 | ENSP00000359735.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183396Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67854
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GnomAD4 exome AF: 0.0000147 AC: 16AN: 1089953Hom.: 0 Cov.: 28 AF XY: 0.0000169 AC XY: 6AN XY: 355641
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GnomAD4 genome Cov.: 23
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at