18-45372456-C-T

Position:

• chr18-45372456-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.-124-110777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,202 control chromosomes in the GnomAD database, including 209 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 0.046 (209 hom., cov: 33)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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:):

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 (SAS) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-110777C>T		intron_variant			NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-110777C>T		intron_variant			NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-110777C>T		intron_variant			XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-110777C>T		intron_variant		2		ENSP00000465953.1

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7036 AN: 152082 Hom.: 209 Cov.: 33

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0463 AC: 7043 AN: 152202 Hom.: 209 Cov.: 33 AF XY: 0.0457 AC XY: 3401 AN XY: 74406

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.0592

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0559 Hom.: 218

Bravo AF: 0.0441

Asia WGS AF: 0.0640 AC: 222 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	0.70
DANN	Benign	0.57

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: rs16978354; hg19: chr18-42952421;