18-45651657-G-A

Variant names:

• chr18-45651657-G-A
• rs4890568
• NM_007163.4:c.1351+7497G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007163.4(SLC14A2):​c.1351+7497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,238 control chromosomes in the GnomAD database, including 65,311 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 0.93 (65311 hom., cov: 31)
• Consequence: SLC14A2 NM_007163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	NM_007163.4	MANE Select	c.1351+7497G>A		intron	N/A	NP_009094.3
	SLC14A2	NM_001242692.2		c.1351+7497G>A		intron	N/A	NP_001229621.1
	SLC14A2	NM_001371319.1		c.1351+7497G>A		intron	N/A	NP_001358248.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	ENST00000255226.11	TSL:1 MANE Select	c.1351+7497G>A		intron	N/A	ENSP00000255226.5
	SLC14A2	ENST00000586448.5	TSL:2	c.1351+7497G>A		intron	N/A	ENSP00000465953.1
	ENSG00000287943	ENST00000729208.1		n.228+37092C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140777 AN: 152120 Hom.: 65262 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.925 AC: 140886 AN: 152238 Hom.: 65311 Cov.: 31 AF XY: 0.921 AC XY: 68573 AN XY: 74426

African (AFR) AF: 0.930 AC: 38618 AN: 41532

American (AMR) AF: 0.908 AC: 13887 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3344 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4010 AN: 5174

South Asian (SAS) AF: 0.931 AC: 4494 AN: 4826

European-Finnish (FIN) AF: 0.877 AC: 9291 AN: 10598

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64170 AN: 68022

Other (OTH) AF: 0.938 AC: 1982 AN: 2112

Alfa AF: 0.938 Hom.: 218384

Bravo AF: 0.926

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		-0.031
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: rs4890568; hg19: chr18-43231622;