rs10502868

Variant names:

• chr18-45573984-T-C
• rs10502868
• ENST00000656053.1:n.1140A>G

Variant summary

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

The ENST00000656053.1(ENSG00000267193):​n.1140A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.062 in 152,308 control chromosomes in the GnomAD database, including 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 0.062 (311 hom., cov: 33)
• Consequence: ENSG00000267193 ENST00000656053.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 9 publications found

Genes affected

ENSG00000267193 (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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-34-50647T>C		intron_variant	Intron 2 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-34-50647T>C		intron_variant	Intron 5 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-34-50647T>C		intron_variant	Intron 3 of 21		XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267193	ENST00000656053.1	n.1140A>G		non_coding_transcript_exon_variant	Exon 2 of 2
SLC14A2	ENST00000586448.5	c.-34-50647T>C		intron_variant	Intron 2 of 20	2		ENSP00000465953.1
ENSG00000287943	ENST00000658918.1	n.77-2479A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0619 AC: 9424 AN: 152190 Hom.: 309 Cov.: 33

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0310

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0620 AC: 9443 AN: 152308 Hom.: 311 Cov.: 33 AF XY: 0.0612 AC XY: 4559 AN XY: 74492

African (AFR) AF: 0.0776 AC: 3225 AN: 41558

American (AMR) AF: 0.0388 AC: 594 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 88 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4830

European-Finnish (FIN) AF: 0.0664 AC: 705 AN: 10616

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4476 AN: 68018

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0614 Hom.: 734

Bravo AF: 0.0611

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		1.5
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: rs10502868; hg19: chr18-43153949;