rs2885618

Variant names:

• chr18-45410876-G-A
• rs2885618
• NM_001242692.2:c.-124-72357G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_001242692.2(SLC14A2):​c.-124-72357G>A variant causes a intron 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 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 2 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]

SLC14A2-AS1 (HGNC:51125): (SLC14A2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-72357G>A		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-72357G>A		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-72357G>A		intron_variant	Intron 2 of 21		XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-72357G>A		intron_variant	Intron 1 of 20	2		ENSP00000465953.1

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

African (AFR) AF: 0.470 AC: 19486 AN: 41472

American (AMR) AF: 0.227 AC: 3466 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3466

East Asian (EAS) AF: 0.171 AC: 883 AN: 5172

South Asian (SAS) AF: 0.141 AC: 678 AN: 4818

European-Finnish (FIN) AF: 0.110 AC: 1161 AN: 10594

Middle Eastern (MID) AF: 0.169 AC: 49 AN: 290

European-Non Finnish (NFE) AF: 0.107 AC: 7246 AN: 68012

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.152 Hom.: 3907

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
PhyloP100		-1.6
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: rs2885618; hg19: chr18-42990841;