18-45220183-C-T

Position:

• chr18-45220183-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+6992C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,976 control chromosomes in the GnomAD database, including 8,261 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 0.32 (8261 hom., cov: 32)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-125+6992C>T		intron_variant			NP_001229621.1
SLC14A2	NM_001371319.1	c.-125+6992C>T		intron_variant			NP_001358248.1
SLC14A2	XM_017026016.3	c.-125+6992C>T		intron_variant			XP_016881505.1
SLC14A2	XM_024451270.2	c.-125+6992C>T		intron_variant			XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-125+6992C>T		intron_variant		2		ENSP00000465953	P1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48272 AN: 151858 Hom.: 8239 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.318 AC: 48331 AN: 151976 Hom.: 8261 Cov.: 32 AF XY: 0.313 AC XY: 23246 AN XY: 74290

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.281

Alfa AF: 0.282 Hom.: 5272

Bravo AF: 0.329

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.7
DANN	Benign	0.71

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: rs10502861; hg19: chr18-42800148;