NM_001242692.2:c.-125+6992C>T

Variant names:

• chr18-45220183-C-T
• rs10502861
• NM_001242692.2:c.-125+6992C>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+6992C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,976 control chromosomes in the GnomAD database, including 8,261 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 0.32 (8261 hom., cov: 32)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 20 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242692.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	NM_001242692.2		c.-125+6992C>T		intron	N/A	NP_001229621.1	Q15849-1
	SLC14A2	NM_001371319.1		c.-125+6992C>T		intron	N/A	NP_001358248.1	Q15849-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A2	ENST00000586448.5	TSL:2	c.-125+6992C>T		intron	N/A	ENSP00000465953.1	Q15849-1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48272 AN: 151858 Hom.: 8239 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.318 AC: 48331 AN: 151976 Hom.: 8261 Cov.: 32 AF XY: 0.313 AC XY: 23246 AN XY: 74290

African (AFR) AF: 0.455 AC: 18853 AN: 41426

American (AMR) AF: 0.297 AC: 4533 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3472

East Asian (EAS) AF: 0.175 AC: 903 AN: 5168

South Asian (SAS) AF: 0.200 AC: 960 AN: 4812

European-Finnish (FIN) AF: 0.240 AC: 2533 AN: 10572

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18503 AN: 67938

Other (OTH) AF: 0.281 AC: 593 AN: 2110

Alfa AF: 0.289 Hom.: 17617

Bravo AF: 0.329

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.7
DANN	Benign	0.71
PhyloP100		-0.020
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: rs10502861; hg19: chr18-42800148;