1-173528878-C-T

Position:

• chr1-173528878-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.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

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]

SLC9C2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9C2	NM_178527.4	c.2313+1027G>A		intron_variant		ENST00000367714.4	NP_848622.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9C2	ENST00000367714.4	c.2313+1027G>A		intron_variant		1	NM_178527.4	ENSP00000356687.3
SLC9C2	ENST00000466087.1	n.1647+1027G>A		intron_variant		1
SLC9C2	ENST00000648789.1	n.918+1027G>A		intron_variant

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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.477

Alfa AF: 0.428 Hom.: 6775

Bravo AF: 0.531

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.013
DANN	Benign	0.63

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: rs1461024; hg19: chr1-173498017;