rs2243787

Positions:

• chr18-45377082-C-A
• chr18-45377082-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066352.1(SLC14A2-AS1):​n.9241-9676G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,932 control chromosomes in the GnomAD database, including 24,266 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 0.52 (24266 hom., cov: 31)
• Consequence: SLC14A2-AS1 XR_007066352.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

SLC14A2-AS1 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A2-AS1	XR_007066352.1	n.9241-9676G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-106151C>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79091 AN: 151816 Hom.: 24204 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.521 AC: 79217 AN: 151932 Hom.: 24266 Cov.: 31 AF XY: 0.510 AC XY: 37907 AN XY: 74268

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.479

Alfa AF: 0.453 Hom.: 3636

Bravo AF: 0.538

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.31

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: rs2243787; hg19: chr18-42957047;