rs990278

Positions:

• chr18-45229957-C-A
• chr18-45229957-C-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+16766C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,026 control chromosomes in the GnomAD database, including 952 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 0.11 (952 hom., cov: 33)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A2	NM_001242692.2	c.-125+16766C>A		intron_variant
SLC14A2	NM_001371319.1	c.-125+16766C>A		intron_variant
SLC14A2	XM_017026016.3	c.-125+16766C>A		intron_variant
SLC14A2	XM_024451270.2	c.-125+16766C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-125+16766C>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16314 AN: 151908 Hom.: 950 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.107 AC: 16325 AN: 152026 Hom.: 952 Cov.: 33 AF XY: 0.106 AC XY: 7868 AN XY: 74342

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0653

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0811

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0749 Hom.: 303

Bravo AF: 0.117

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.60
DANN	Benign	0.34

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: rs990278; hg19: chr18-42809922;