rs7801190

Positions:

• chr7-100860471-C-G

Variant summary

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

The NM_020246.4(SLC12A9):​c.1218+239C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 551,228 control chromosomes in the GnomAD database, including 2,107 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 0.096 (1247 hom., cov: 33)
  • Exomes 𝑓: 0.053 (860 hom.)
• Consequence: SLC12A9 NM_020246.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

Genes affected

SLC12A9 (HGNC:17435): (solute carrier family 12 member 9) Predicted to enable potassium:chloride symporter activity. Predicted to be involved in cell volume homeostasis; inorganic ion homeostasis; and inorganic ion transmembrane transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SLC12A9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A9	NM_020246.4	c.1218+239C>G		intron_variant		ENST00000354161.8	NP_064631.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A9	ENST00000354161.8	c.1218+239C>G		intron_variant		1	NM_020246.4	ENSP00000275730.4

Frequencies

GnomAD3 genomes AF: 0.0958 AC: 14530 AN: 151656 Hom.: 1241 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.000585

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0994

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0985

GnomAD4 exome AF: 0.0525 AC: 20977 AN: 399454 Hom.: 860 Cov.: 3 AF XY: 0.0536 AC XY: 11249 AN XY: 210060

Gnomad4 AFR exome AF: 0.216

Gnomad4 AMR exome AF: 0.0516

Gnomad4 ASJ exome AF: 0.0987

Gnomad4 EAS exome AF: 0.000260

Gnomad4 SAS exome AF: 0.0627

Gnomad4 FIN exome AF: 0.0301

Gnomad4 NFE exome AF: 0.0476

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.0960 AC: 14563 AN: 151774 Hom.: 1247 Cov.: 33 AF XY: 0.0935 AC XY: 6930 AN XY: 74152

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.000586

Gnomad4 SAS AF: 0.0611

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0555 Hom.: 182

Bravo AF: 0.103

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.54

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: rs7801190; hg19: chr7-100458093;