rs2885618

Positions:

• chr18-45410876-G-A
• chr18-45410876-G-C
• chr18-45410876-G-T

Variant summary

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

The XR_007066352.1(SLC14A2-AS1):​n.9240+24323C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,132 control chromosomes in the GnomAD database, including 5,752 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 0.22 (5752 hom., cov: 33)
• Consequence: SLC14A2-AS1 XR_007066352.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

SLC14A2-AS1 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2-AS1	XR_007066352.1	n.9240+24323C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-72357G>A		intron_variant		2		ENSP00000465953	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33802 AN: 152016 Hom.: 5745 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.223 AC: 33855 AN: 152132 Hom.: 5752 Cov.: 33 AF XY: 0.220 AC XY: 16335 AN XY: 74378

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.215

Alfa AF: 0.132 Hom.: 1917

Bravo AF: 0.246

Asia WGS AF: 0.164 AC: 570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.76

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: rs2885618; hg19: chr18-42990841;