rs6675929

Variant names:

• chr1-173519147-C-T
• rs6675929
• NM_178527.4:c.2740-1443G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178527.4(SLC9C2):​c.2740-1443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,734 control chromosomes in the GnomAD database, including 4,211 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 0.20 (4211 hom., cov: 31)
• Consequence: SLC9C2 NM_178527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 4 publications found

Genes affected

SLC9C2 (HGNC:28664): (solute carrier family 9 member C2 (putative)) Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178527.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9C2	NM_178527.4	MANE Select	c.2740-1443G>A		intron	N/A	NP_848622.2	Q5TAH2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9C2	ENST00000367714.4	TSL:1 MANE Select	c.2740-1443G>A		intron	N/A	ENSP00000356687.3	Q5TAH2
	SLC9C2	ENST00000466087.1	TSL:1	n.2074-1443G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30422 AN: 151616 Hom.: 4209 Cov.: 31

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.201 AC: 30427 AN: 151734 Hom.: 4211 Cov.: 31 AF XY: 0.209 AC XY: 15511 AN XY: 74112

African (AFR) AF: 0.0656 AC: 2717 AN: 41400

American (AMR) AF: 0.325 AC: 4946 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3266 AN: 5082

South Asian (SAS) AF: 0.369 AC: 1768 AN: 4794

European-Finnish (FIN) AF: 0.214 AC: 2253 AN: 10530

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14389 AN: 67938

Other (OTH) AF: 0.211 AC: 443 AN: 2102

Alfa AF: 0.213 Hom.: 1982

Bravo AF: 0.202

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6675929; hg19: chr1-173488286;