rs1054986

Positions:

• chr18-45438299-T-C
• chr18-45438299-T-G

Variant summary

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

The NM_001242692.2(SLC14A2):​c.-124-44934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,070 control chromosomes in the GnomAD database, including 11,581 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 0.35 (11581 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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:51125): (SLC14A2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-44934T>C		intron_variant			NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-44934T>C		intron_variant			NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-44934T>C		intron_variant			XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-44934T>C		intron_variant		2		ENSP00000465953.1
SLC14A2-AS1	ENST00000592286.1	n.415A>G		non_coding_transcript_exon_variant	2/2	4
SLC14A2-AS1	ENST00000592899.1	n.234A>G		non_coding_transcript_exon_variant	3/3	3
SLC14A2-AS1	ENST00000585759.1	n.245-1581A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53982 AN: 151952 Hom.: 11582 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.373

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.355 AC: 53971 AN: 152070 Hom.: 11581 Cov.: 32 AF XY: 0.355 AC XY: 26365 AN XY: 74326

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.370

Alfa AF: 0.395 Hom.: 5763

Bravo AF: 0.339

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.73

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: rs1054986; hg19: chr18-43018264;