rs651630

chr3-125092470-G-A

Variant summary

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

The NM_024628.6(SLC12A8):c.1706-272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,012 control chromosomes in the GnomAD database, including 13,805 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 0.41 (13805 hom., cov: 31)
• Consequence: SLC12A8 NM_024628.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A8	NM_024628.6	c.1706-272C>T		intron_variant		ENST00000469902.6
SLC12A8	NM_001195483.2	c.1706-272C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A8	ENST00000469902.6	c.1706-272C>T		intron_variant		2	NM_024628.6	P1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61853 AN: 151894 Hom.: 13810 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.407 AC: 61870 AN: 152012 Hom.: 13805 Cov.: 31 AF XY: 0.408 AC XY: 30285 AN XY: 74280

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.419

Alfa AF: 0.479 Hom.: 26587

Bravo AF: 0.388

Asia WGS AF: 0.512 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.85
Dann	Benign	0.24

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: rs651630; hg19: chr3-124811314; COSMIC: COSV58864471;