rs12904216

Positions:

• chr15-48231070-A-G

Variant summary

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

The NM_000338.3(SLC12A1):​c.975+567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,136 control chromosomes in the GnomAD database, including 33,991 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 0.63 (33991 hom., cov: 32)
• Consequence: SLC12A1 NM_000338.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

SLC12A1 (HGNC:10910): (solute carrier family 12 member 1) This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle's loop and the macula densa. It plays a key role in concentrating urine and accounts for most of the NaCl resorption. It is sensitive to such diuretics as furosemide and bumetanide. Some Bartter-like syndromes result from defects in this gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity in humans has not been experimentally proven.[provided by RefSeq, May 2010]

SLC12A1 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A1	NM_000338.3	c.975+567A>G		intron_variant		ENST00000380993.8	NP_000329.2
SLC12A1	NM_001184832.2	c.975+567A>G		intron_variant			NP_001171761.1
SLC12A1	NM_001384136.1	c.975+567A>G		intron_variant			NP_001371065.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A1	ENST00000380993.8	c.975+567A>G		intron_variant		5	NM_000338.3	ENSP00000370381.3

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95213 AN: 152016 Hom.: 34006 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.626 AC: 95208 AN: 152136 Hom.: 33991 Cov.: 32 AF XY: 0.629 AC XY: 46756 AN XY: 74356

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.659

Alfa AF: 0.761 Hom.: 42668

Bravo AF: 0.602

Asia WGS AF: 0.527 AC: 1836 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	0.047
DANN	Benign	0.29

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: rs12904216; hg19: chr15-48523267;