chr1-173528878-C-T

Variant names:

• chr1-173528878-C-T
• rs1461024
• NM_178527.4:c.2313+1027G>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.2313+1027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,978 control chromosomes in the GnomAD database, including 21,319 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 0.51 (21319 hom., cov: 31)
• Consequence: SLC9C2 NM_178527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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.2313+1027G>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.2313+1027G>A		intron	N/A	ENSP00000356687.3	Q5TAH2
	SLC9C2	ENST00000466087.1	TSL:1	n.1647+1027G>A		intron	N/A
	SLC9C2	ENST00000648789.1		n.918+1027G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77039 AN: 151860 Hom.: 21265 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.508 AC: 77157 AN: 151978 Hom.: 21319 Cov.: 31 AF XY: 0.510 AC XY: 37883 AN XY: 74248

African (AFR) AF: 0.665 AC: 27544 AN: 41430

American (AMR) AF: 0.549 AC: 8383 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4928 AN: 5174

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4814

European-Finnish (FIN) AF: 0.352 AC: 3711 AN: 10536

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27259 AN: 67972

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.430 Hom.: 7668

Bravo AF: 0.531

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.013
DANN	Benign	0.63
PhyloP100		-3.0
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: rs1461024; hg19: chr1-173498017;