rs9304318

chr18-45654835-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A2	NM_007163.4	c.1352-8950G>A		intron_variant		ENST00000255226.11
LOC105372093	XR_935423.3	n.873-17678C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A2	ENST00000255226.11	c.1352-8950G>A		intron_variant		1	NM_007163.4	P1
SLC14A2	ENST00000586448.5	c.1352-8950G>A		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.785

Alfa AF: 0.757 Hom.: 3826

Bravo AF: 0.740

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.8
Dann	Benign	0.56

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: rs9304318; hg19: chr18-43234800;