rs8118160

Positions:

• chr20-49818099-A-G
• chr20-49818099-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015266.3(SLC9A8):​c.208+2910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,990 control chromosomes in the GnomAD database, including 24,476 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (24476 hom., cov: 31)
• Consequence: SLC9A8 NM_015266.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

Genes affected

SLC9A8 (HGNC:20728): (solute carrier family 9 member A8) Sodium-hydrogen exchangers (NHEs), such as SLC9A8, are integral transmembrane proteins that exchange extracellular Na+ for intracellular H+. NHEs have multiple functions, including intracellular pH homeostasis, cell volume regulation, and electroneutral NaCl absorption in epithelia (Xu et al., 2008 [PubMed 18209477]).[supplied by OMIM, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9A8	NM_015266.3	c.208+2910A>G		intron_variant		ENST00000361573.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9A8	ENST00000361573.3	c.208+2910A>G		intron_variant		1	NM_015266.3	P1
SLC9A8	ENST00000417961.5	c.208+2910A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83129 AN: 151872 Hom.: 24451 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.546

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.547 AC: 83205 AN: 151990 Hom.: 24476 Cov.: 31 AF XY: 0.533 AC XY: 39611 AN XY: 74272

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.544

Alfa AF: 0.506 Hom.: 32641

Bravo AF: 0.565

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
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

Publications

LitVar

Other links and lift over

dbSNP: rs8118160; hg19: chr20-48434636;