18-45286505-A-C

Variant names:

• chr18-45286505-A-C
• rs1551821
• NM_001242692.2:c.-125+73314A>C

Variant summary

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

The NM_001242692.2(SLC14A2):​c.-125+73314A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,092 control chromosomes in the GnomAD database, including 6,583 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 0.26 (6583 hom., cov: 32)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242692.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	NM_001242692.2		c.-125+73314A>C		intron	N/A	NP_001229621.1	Q15849-1
	SLC14A2	NM_001371319.1		c.-125+73314A>C		intron	N/A	NP_001358248.1	Q15849-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	ENST00000586448.5	TSL:2	c.-125+73314A>C		intron	N/A	ENSP00000465953.1	Q15849-1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39491 AN: 151974 Hom.: 6558 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.260 AC: 39565 AN: 152092 Hom.: 6583 Cov.: 32 AF XY: 0.258 AC XY: 19177 AN XY: 74382

African (AFR) AF: 0.479 AC: 19841 AN: 41432

American (AMR) AF: 0.199 AC: 3035 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4820

European-Finnish (FIN) AF: 0.130 AC: 1382 AN: 10602

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11290 AN: 67994

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.179 Hom.: 2233

Bravo AF: 0.275

Asia WGS AF: 0.293 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.22
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: rs1551821; hg19: chr18-42866470;