18-45607165-A-G

Variant summary

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

The XR_935423.3(LOC105372093):n.5745T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,038 control chromosomes in the GnomAD database, including 37,398 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 0.70 (37398 hom., cov: 31)
• Consequence: LOC105372093 XR_935423.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

Genes affected

LOC105372093 (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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372093	XR_935423.3	n.5745T>C		non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658918.1	n.76+4300T>C		intron_variant, non_coding_transcript_variant
SLC14A2	ENST00000586448.5	c.-34-17466A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106086 AN: 151920 Hom.: 37370 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.698 AC: 106165 AN: 152038 Hom.: 37398 Cov.: 31 AF XY: 0.699 AC XY: 51978 AN XY: 74318

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.696

Alfa AF: 0.710 Hom.: 18043

Bravo AF: 0.699

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	7.2
Dann	Benign	0.79

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: rs7227483; hg19: chr18-43187130;