rs4890568

Positions:

• chr18-45651657-G-A
• chr18-45651657-G-C

Variant summary

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

The NM_007163.4(SLC14A2):​c.1351+7497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,238 control chromosomes in the GnomAD database, including 65,311 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 0.93 (65311 hom., cov: 31)
• Consequence: SLC14A2 NM_007163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_007163.4	c.1351+7497G>A		intron_variant		ENST00000255226.11	NP_009094.3
LOC105372093	XR_935423.3	n.873-14500C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000255226.11	c.1351+7497G>A		intron_variant		1	NM_007163.4	ENSP00000255226	P1
SLC14A2	ENST00000586448.5	c.1351+7497G>A		intron_variant		2		ENSP00000465953	P1

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140777 AN: 152120 Hom.: 65262 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.925 AC: 140886 AN: 152238 Hom.: 65311 Cov.: 31 AF XY: 0.921 AC XY: 68573 AN XY: 74426

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.938

Alfa AF: 0.940 Hom.: 99023

Bravo AF: 0.926

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.53

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: rs4890568; hg19: chr18-43231622;