3-112246399-T-G

Variant names:

• chr3-112246399-T-G
• rs9822786
• NM_183061.3:c.1198-2323A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_183061.3(SLC9C1):​c.1198-2323A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,036 control chromosomes in the GnomAD database, including 27,122 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 0.59 (27122 hom., cov: 32)
• Consequence: SLC9C1 NM_183061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 4 publications found

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]

LOC100532749 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183061.3. 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
	SLC9C1	NM_183061.3	MANE Select	c.1198-2323A>C		intron	N/A	NP_898884.1	Q4G0N8-1
	SLC9C1	NM_001320531.2		c.1054-2323A>C		intron	N/A	NP_001307460.1	Q4G0N8-2
	SLC9C1	NR_135297.2		n.932-6393A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9C1	ENST00000305815.10	TSL:2 MANE Select	c.1198-2323A>C		intron	N/A	ENSP00000306627.5	Q4G0N8-1
	SLC9C1	ENST00000487372.5	TSL:1	c.1054-2323A>C		intron	N/A	ENSP00000420688.1	Q4G0N8-2
	SLC9C1	ENST00000471295.1	TSL:5	n.717-6393A>C		intron	N/A	ENSP00000418371.1	F8WCJ0

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89872 AN: 151918 Hom.: 27101 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.592 AC: 89931 AN: 152036 Hom.: 27122 Cov.: 32 AF XY: 0.592 AC XY: 44011 AN XY: 74310

African (AFR) AF: 0.487 AC: 20182 AN: 41458

American (AMR) AF: 0.682 AC: 10419 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4059 AN: 5154

South Asian (SAS) AF: 0.727 AC: 3503 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5758 AN: 10576

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42139 AN: 67982

Other (OTH) AF: 0.602 AC: 1267 AN: 2104

Alfa AF: 0.618 Hom.: 34584

Bravo AF: 0.596

Asia WGS AF: 0.742 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.69
PhyloP100		-0.44
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: rs9822786; hg19: chr3-111965246;