rs7232775

Positions:

• chr18-45622439-C-T

Variant summary

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

The NM_007163.4(SLC14A2):​c.-34-2192C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,990 control chromosomes in the GnomAD database, including 44,572 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 0.76 (44572 hom., cov: 30)
• Consequence: SLC14A2 NM_007163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

SLC14A2 (HGNC:10919): (solute carrier family 14 member 2) The protein encoded by this gene belongs to the urea transporter family. In mammalian cells, urea is the chief end product of nitrogen catabolism, and plays an important role in the urinary concentration mechanism. This protein is expressed in the inner medulla of the kidney, and mediates rapid transepithelial urea transport across the inner medullary collecting duct. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2011]

LOC105372093 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_007163.4	c.-34-2192C>T		intron_variant		ENST00000255226.11	NP_009094.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000255226.11	c.-34-2192C>T		intron_variant		1	NM_007163.4	ENSP00000255226.5
SLC14A2	ENST00000586448.5	c.-34-2192C>T		intron_variant		2		ENSP00000465953.1
SLC14A2	ENST00000323329.3	n.-34-2192C>T		intron_variant		2		ENSP00000320689.3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115525 AN: 151872 Hom.: 44508 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.761 AC: 115644 AN: 151990 Hom.: 44572 Cov.: 30 AF XY: 0.761 AC XY: 56466 AN XY: 74242

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.725

Alfa AF: 0.710 Hom.: 73727

Bravo AF: 0.770

Asia WGS AF: 0.812 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.57

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: rs7232775; hg19: chr18-43202404;