rs1484874

chr18-45630229-G-Achr18-45630229-G-Cchr18-45630229-G-T

Variant summary

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

The NM_007163.4(SLC14A2):c.522-2121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,014 control chromosomes in the GnomAD database, including 10,520 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 0.37 (10520 hom., cov: 32)
• Consequence: SLC14A2 NM_007163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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]

LOC105372093 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A2	NM_007163.4	c.522-2121G>A		intron_variant		ENST00000255226.11
LOC105372093	XR_935423.3	n.1207+6594C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A2	ENST00000255226.11	c.522-2121G>A		intron_variant		1	NM_007163.4	P1
SLC14A2	ENST00000586448.5	c.522-2121G>A		intron_variant		2		P1
SLC14A2	ENST00000323329.3	c.522-2121G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55760 AN: 151896 Hom.: 10498 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.367 AC: 55823 AN: 152014 Hom.: 10520 Cov.: 32 AF XY: 0.363 AC XY: 26940 AN XY: 74294

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.414

Alfa AF: 0.391 Hom.: 7195

Bravo AF: 0.367

Asia WGS AF: 0.332 AC: 1154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.63
Dann	Benign	0.21

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: rs1484874; hg19: chr18-43210194;