rs2243787

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007066352.1(SLC14A2-AS1):​n.9241-9676G>T variant causes a intron, non coding transcript 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-AS1
XR_007066352.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
SLC14A2-AS1XR_007066352.1 linkuse as main transcriptn.9241-9676G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC14A2ENST00000586448.5 linkuse as main transcriptc.-124-106151C>A intron_variant 2 P1Q15849-1

Frequencies

GnomAD3 genomes
AF:
0.521
AC:
79091
AN:
151816
Hom.:
24204
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.862
Gnomad4 AMR
AF:
0.396
Gnomad4 ASJ
AF:
0.372
Gnomad4 EAS
AF:
0.194
Gnomad4 SAS
AF:
0.477
Gnomad4 FIN
AF:
0.316
Gnomad4 NFE
AF:
0.411
Gnomad4 OTH
AF:
0.479
Alfa
AF:
0.453
Hom.:
3636
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2243787; hg19: chr18-42957047; API