rs990278

Variant names:

• chr18-45229957-C-A
• rs990278
• NM_001242692.2:c.-125+16766C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-45229957-C-A
• chr18-45229957-C-T

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+16766C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,026 control chromosomes in the GnomAD database, including 952 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 0.11 (952 hom., cov: 33)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-125+16766C>A		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-125+16766C>A		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-125+16766C>A		intron_variant	Intron 2 of 21		XP_024307038.1
SLC14A2	XM_017026016.3	c.-125+16766C>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+16766C>A		intron_variant	Intron 1 of 20	2		ENSP00000465953.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16314 AN: 151908 Hom.: 950 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.107 AC: 16325 AN: 152026 Hom.: 952 Cov.: 33 AF XY: 0.106 AC XY: 7868 AN XY: 74342

African (AFR) AF: 0.157 AC: 6516 AN: 41386

American (AMR) AF: 0.137 AC: 2097 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 297 AN: 3444

East Asian (EAS) AF: 0.112 AC: 581 AN: 5178

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4826

European-Finnish (FIN) AF: 0.0556 AC: 590 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0811 AC: 5514 AN: 68006

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0789 Hom.: 455

Bravo AF: 0.117

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.60
DANN	Benign	0.34
PhyloP100		-0.37
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: rs990278; hg19: chr18-42809922;