chr18-45622439-C-T

Variant names:

• chr18-45622439-C-T
• rs7232775
• NM_007163.4:c.-34-2192C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

ENSG00000287943 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007163.4. 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
	SLC14A2	NM_007163.4	MANE Select	c.-34-2192C>T		intron	N/A	NP_009094.3
	SLC14A2	NM_001242692.2		c.-34-2192C>T		intron	N/A	NP_001229621.1
	SLC14A2	NM_001371319.1		c.-34-2192C>T		intron	N/A	NP_001358248.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	ENST00000255226.11	TSL:1 MANE Select	c.-34-2192C>T		intron	N/A	ENSP00000255226.5
	SLC14A2	ENST00000586448.5	TSL:2	c.-34-2192C>T		intron	N/A	ENSP00000465953.1
	SLC14A2	ENST00000323329.3	TSL:2	n.-34-2192C>T		intron	N/A	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

African (AFR) AF: 0.882 AC: 36581 AN: 41476

American (AMR) AF: 0.753 AC: 11498 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2208 AN: 3462

East Asian (EAS) AF: 0.844 AC: 4351 AN: 5158

South Asian (SAS) AF: 0.810 AC: 3892 AN: 4804

European-Finnish (FIN) AF: 0.670 AC: 7057 AN: 10530

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.701 AC: 47658 AN: 67976

Other (OTH) AF: 0.725 AC: 1531 AN: 2112

Alfa AF: 0.721 Hom.: 149594

Bravo AF: 0.770

Asia WGS AF: 0.812 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		0.19
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: rs7232775; hg19: chr18-43202404;