rs1551821

chr18-45286505-A-Cchr18-45286505-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A2	NM_001242692.2	c.-125+73314A>C		intron_variant
SLC14A2	NM_001371319.1	c.-125+73314A>C		intron_variant
SLC14A2	XM_017026016.3	c.-125+73314A>C		intron_variant
SLC14A2	XM_024451270.2	c.-125+73314A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-125+73314A>C		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.245

Alfa AF: 0.177 Hom.: 1549

Bravo AF: 0.275

Asia WGS AF: 0.293 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.43

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: rs1551821; hg19: chr18-42866470;