chr18-45377082-C-A

Variant names:

• chr18-45377082-C-A
• rs2243787
• NM_001242692.2:c.-124-106151C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242692.2(SLC14A2):​c.-124-106151C>A variant causes a intron 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 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-106151C>A		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-106151C>A		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-106151C>A		intron_variant	Intron 2 of 21		XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-124-106151C>A		intron_variant	Intron 1 of 20	2		ENSP00000465953.1

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

African (AFR) AF: 0.862 AC: 35722 AN: 41462

American (AMR) AF: 0.396 AC: 6047 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3468

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5172

South Asian (SAS) AF: 0.477 AC: 2293 AN: 4810

European-Finnish (FIN) AF: 0.316 AC: 3334 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27893 AN: 67900

Other (OTH) AF: 0.479 AC: 1010 AN: 2110

Alfa AF: 0.463 Hom.: 3933

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2243787; hg19: chr18-42957047;