X-136022705-G-T

Variant names:

• chrX-136022705-G-T
• rs6654310
• NM_001379110.1:c.1306+8G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001379110.1(SLC9A6):​c.1306+8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000001 in 995,198 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0000010 (0 hom. 1 hem.)
• Consequence: SLC9A6 NM_001379110.1 splice_region, intron
• Scores: Splicing: ADA: 0.00004423
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 0 publications found

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]

SLC9A6 Gene-Disease associations (from GenCC):

• Christianson syndrome

  Inheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet, ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A6	NM_001379110.1	c.1306+8G>T		splice_region_variant, intron_variant	Intron 12 of 17	ENST00000630721.3	NP_001366039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A6	ENST00000630721.3	c.1306+8G>T		splice_region_variant, intron_variant	Intron 12 of 17	4	NM_001379110.1	ENSP00000487486.2
SLC9A6	ENST00000370695.8	c.1462+8G>T		splice_region_variant, intron_variant	Intron 11 of 15	1		ENSP00000359729.4
SLC9A6	ENST00000370698.7	c.1366+8G>T		splice_region_variant, intron_variant	Intron 11 of 15	1		ENSP00000359732.3
SLC9A6	ENST00000370701.6	c.1306+8G>T		splice_region_variant, intron_variant	Intron 12 of 16	1		ENSP00000359735.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 0.00000100 AC: 1 AN: 995198 Hom.: 0 Cov.: 19 AF XY: 0.00000355 AC XY: 1 AN XY: 282018

African (AFR) AF: 0.00 AC: 0 AN: 24524

American (AMR) AF: 0.00 AC: 0 AN: 34495

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18152

East Asian (EAS) AF: 0.00 AC: 0 AN: 28552

South Asian (SAS) AF: 0.00 AC: 0 AN: 51767

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38430

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3811

European-Non Finnish (NFE) AF: 0.00000133 AC: 1 AN: 753429

Other (OTH) AF: 0.00 AC: 0 AN: 42038

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.45
DANN	Benign	0.59
PhyloP100		-0.20

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000044
dbscSNV1_RF	Benign	0.016
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6654310; hg19: chrX-135104864;