chr18-45229026-G-A

Variant names:

• chr18-45229026-G-A
• rs10502862
• NM_001242692.2:c.-125+15835G>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.-125+15835G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,054 control chromosomes in the GnomAD database, including 4,906 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 0.25 (4906 hom., cov: 33)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-125+15835G>A		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-125+15835G>A		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-125+15835G>A		intron_variant	Intron 2 of 21		XP_024307038.1
SLC14A2	XM_017026016.3	c.-125+15835G>A		intron_variant	Intron 2 of 20		XP_016881505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000586448.5	c.-125+15835G>A		intron_variant	Intron 1 of 20	2		ENSP00000465953.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37279 AN: 151936 Hom.: 4889 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.245 AC: 37323 AN: 152054 Hom.: 4906 Cov.: 33 AF XY: 0.242 AC XY: 18018 AN XY: 74322

African (AFR) AF: 0.343 AC: 14209 AN: 41412

American (AMR) AF: 0.245 AC: 3747 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3468

East Asian (EAS) AF: 0.172 AC: 887 AN: 5170

South Asian (SAS) AF: 0.187 AC: 899 AN: 4814

European-Finnish (FIN) AF: 0.158 AC: 1676 AN: 10604

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14261 AN: 67984

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.191 Hom.: 979

Bravo AF: 0.255

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.75
PhyloP100		-0.52
Mutation Taster		=99/1	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: rs10502862; hg19: chr18-42808991;