chr18-45654835-G-A

Variant names:

• chr18-45654835-G-A
• rs9304318
• NM_007163.4:c.1352-8950G>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.1352-8950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 151,994 control chromosomes in the GnomAD database, including 43,970 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 0.75 (43970 hom., cov: 31)
• Consequence: SLC14A2 NM_007163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 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.1352-8950G>A		intron	N/A	NP_009094.3
	SLC14A2	NM_001242692.2		c.1352-8950G>A		intron	N/A	NP_001229621.1
	SLC14A2	NM_001371319.1		c.1352-8950G>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.1352-8950G>A		intron	N/A	ENSP00000255226.5
	SLC14A2	ENST00000586448.5	TSL:2	c.1352-8950G>A		intron	N/A	ENSP00000465953.1
	ENSG00000287943	ENST00000729208.1		n.228+33914C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114348 AN: 151876 Hom.: 43945 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.753 AC: 114416 AN: 151994 Hom.: 43970 Cov.: 31 AF XY: 0.750 AC XY: 55757 AN XY: 74314

African (AFR) AF: 0.639 AC: 26467 AN: 41416

American (AMR) AF: 0.772 AC: 11785 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2003 AN: 5160

South Asian (SAS) AF: 0.733 AC: 3523 AN: 4804

European-Finnish (FIN) AF: 0.805 AC: 8511 AN: 10578

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.832 AC: 56534 AN: 67988

Other (OTH) AF: 0.785 AC: 1654 AN: 2108

Alfa AF: 0.750 Hom.: 3975

Bravo AF: 0.740

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		-0.12
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: rs9304318; hg19: chr18-43234800;