NM_001242692.2:c.-124-90909A>G

Variant names:

• chr18-45392324-A-G
• rs1421201
• NM_001242692.2:c.-124-90909A>G

Variant summary

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

The NM_001242692.2(SLC14A2):​c.-124-90909A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,898 control chromosomes in the GnomAD database, including 19,077 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 0.50 (19077 hom., cov: 31)
• Consequence: SLC14A2 NM_001242692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• 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]

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-90909A>G		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-90909A>G		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-90909A>G		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.-124-90909A>G		intron_variant	Intron 1 of 20	2		ENSP00000465953.1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75859 AN: 151780 Hom.: 19085 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.499 AC: 75870 AN: 151898 Hom.: 19077 Cov.: 31 AF XY: 0.499 AC XY: 37045 AN XY: 74238

African (AFR) AF: 0.465 AC: 19262 AN: 41398

American (AMR) AF: 0.477 AC: 7283 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1697 AN: 3464

East Asian (EAS) AF: 0.459 AC: 2356 AN: 5138

South Asian (SAS) AF: 0.671 AC: 3235 AN: 4818

European-Finnish (FIN) AF: 0.497 AC: 5257 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34954 AN: 67930

Other (OTH) AF: 0.505 AC: 1068 AN: 2114

Alfa AF: 0.511 Hom.: 44419

Bravo AF: 0.495

Asia WGS AF: 0.553 AC: 1927 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	0.62
DANN	Benign	0.66
PhyloP100		-0.47
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: rs1421201; hg19: chr18-42972289; COSMIC: COSV73945262;