rs6675929

chr1-173519147-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9C2	NM_178527.4	c.2740-1443G>A		intron_variant		ENST00000367714.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9C2	ENST00000367714.4	c.2740-1443G>A		intron_variant		1	NM_178527.4	P1
SLC9C2	ENST00000466087.1	n.2074-1443G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0656

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.211

Alfa AF: 0.213 Hom.: 1793

Bravo AF: 0.202

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.54

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: rs6675929; hg19: chr1-173488286;