rs9834177

Variant names:

• chr3-125089686-C-T
• rs9834177
• NM_024628.6:c.1922-1316G>A

Variant summary

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

The NM_024628.6(SLC12A8):​c.1922-1316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.20 (769 hom., cov: 10)
• Consequence: SLC12A8 NM_024628.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 1 publications found

Genes affected

SLC12A8 (HGNC:15595): (solute carrier family 12 member 8) This gene is thought to be a candidate for psoriasis susceptibility. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Sep 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024628.6. 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
	SLC12A8	NM_024628.6	MANE Select	c.1922-1316G>A		intron	N/A	NP_078904.4
	SLC12A8	NM_001195483.2		c.1922-1316G>A		intron	N/A	NP_001182412.2	A0AV02-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A8	ENST00000469902.6	TSL:2 MANE Select	c.1922-1316G>A		intron	N/A	ENSP00000418783.1	A0AV02-1
	SLC12A8	ENST00000393469.8	TSL:1	c.1922-1316G>A		intron	N/A	ENSP00000377112.4	A0AV02-1
	SLC12A8	ENST00000430155.6	TSL:1	c.1325-1316G>A		intron	N/A	ENSP00000415713.2	A0AV02-3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 11931 AN: 60522 Hom.: 767 Cov.: 10

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0893

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.197 AC: 11936 AN: 60526 Hom.: 769 Cov.: 10 AF XY: 0.194 AC XY: 5515 AN XY: 28388

African (AFR) AF: 0.299 AC: 5196 AN: 17392

American (AMR) AF: 0.208 AC: 1168 AN: 5602

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 275 AN: 1364

East Asian (EAS) AF: 0.456 AC: 631 AN: 1384

South Asian (SAS) AF: 0.220 AC: 260 AN: 1180

European-Finnish (FIN) AF: 0.0453 AC: 138 AN: 3044

Middle Eastern (MID) AF: 0.154 AC: 12 AN: 78

European-Non Finnish (NFE) AF: 0.139 AC: 4088 AN: 29352

Other (OTH) AF: 0.174 AC: 138 AN: 794

Alfa AF: 0.101 Hom.: 82

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.64
PhyloP100		-0.33
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: rs9834177; hg19: chr3-124808530;