3-112202973-C-T

Variant summary

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

The NM_183061.3(SLC9C1):c.2173-574G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,816 control chromosomes in the GnomAD database, including 7,212 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 0.30 (7212 hom., cov: 31)
• Consequence: SLC9C1 NM_183061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

SLC9C1 (HGNC:31401): (solute carrier family 9 member C1) 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 act upstream of or within flagellated sperm motility. Predicted to be located in motile cilium. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC124909407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9C1	NM_183061.3	c.2173-574G>A		intron_variant		ENST00000305815.10
LOC124909407	XR_007096003.1	n.7373C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9C1	ENST00000305815.10	c.2173-574G>A		intron_variant		2	NM_183061.3	P1
SLC9C1	ENST00000487372.5	c.2029-574G>A		intron_variant		1
SLC9C1	ENST00000471295.1	c.*502-574G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45976 AN: 151698 Hom.: 7196 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.303 AC: 46027 AN: 151816 Hom.: 7212 Cov.: 31 AF XY: 0.302 AC XY: 22389 AN XY: 74194

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.266

Alfa AF: 0.287 Hom.: 2638

Bravo AF: 0.311

Asia WGS AF: 0.334 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.7
Dann	Benign	0.44

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: rs2029637; hg19: chr3-111921820;