rs6691482

chr1-173573725-T-C

Variant summary

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

The NM_178527.4(SLC9C2):c.903-400A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,070 control chromosomes in the GnomAD database, including 24,938 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 (24938 hom., cov: 32)
• Consequence: SLC9C2 NM_178527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9C2	NM_178527.4	c.903-400A>G		intron_variant		ENST00000367714.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9C2	ENST00000367714.4	c.903-400A>G		intron_variant		1	NM_178527.4	P1
	ENST00000431459.1	n.68+18407T>C		intron_variant, non_coding_transcript_variant		5
SLC9C2	ENST00000466087.1	n.92-400A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83210 AN: 151952 Hom.: 24889 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.548 AC: 83318 AN: 152070 Hom.: 24938 Cov.: 32 AF XY: 0.549 AC XY: 40849 AN XY: 74346

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.520

Alfa AF: 0.462 Hom.: 9899

Bravo AF: 0.574

Asia WGS AF: 0.708 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.41

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: rs6691482; hg19: chr1-173542864;