rs782665428
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001379110.1(SLC9A6):c.1863G>A(p.Pro621=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,208,782 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 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 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.0000073 ( 0 hom. 3 hem. )
Consequence
SLC9A6
NM_001379110.1 synonymous
NM_001379110.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant X-136044547-G-A is Benign according to our data. Variant chrX-136044547-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 586616.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.1863G>A | p.Pro621= | synonymous_variant | 18/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.1863G>A | p.Pro621= | synonymous_variant | 18/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000898 AC: 1AN: 111337Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33557
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GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183344Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67808
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GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097445Hom.: 0 Cov.: 30 AF XY: 0.00000827 AC XY: 3AN XY: 362817
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GnomAD4 genome ? AF: 0.00000898 AC: 1AN: 111337Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33557
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 23, 2018 | - - |
Christianson syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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