Variant rs1123617 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007163.4(SLC14A2):c.2248G>A(p.Val750Ile) variant causes a missense change. The variant allele was found at a frequency of 0.154 in 1,613,224 control chromosomes in the GnomAD database, including 20,173 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1633 hom., cov: 32)

Exomes 𝑓: 0.16 ( 18540 hom. )

Consequence

SLC14A2
NM_007163.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.01

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]

SLC14A2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036180615).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A2	NM_007163.4 linkuse as main transcript	c.2248G>A	p.Val750Ile	missense_variant	17/20	ENST00000255226.11	NP_009094.3
LOC105372093	XR_935423.3 linkuse as main transcript	n.872+19477C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000255226.11 linkuse as main transcript	c.2248G>A	p.Val750Ile	missense_variant	17/20	1	NM_007163.4	ENSP00000255226	P1	Q15849-1
	ENST00000589510.5 linkuse as main transcript	n.207-3445C>T		intron_variant, non_coding_transcript_variant		5
SLC14A2	ENST00000586448.5 linkuse as main transcript	c.2248G>A	p.Val750Ile	missense_variant	18/21	2		ENSP00000465953	P1	Q15849-1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21251

AN:

152076

Hom.:

1628

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0842

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.166

AC:

41508

AN:

250678

Hom.:

3795

AF XY:

0.167

AC XY:

22655

AN XY:

135438

show subpopulations

Gnomad AFR exome

AF:

0.0853

Gnomad AMR exome

AF:

0.180

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.284

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.137

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.156

AC:

227942

AN:

1461030

Hom.:

18540

Cov.:

AF XY:

0.157

AC XY:

114242

AN XY:

726822

show subpopulations

Gnomad4 AFR exome

AF:

0.0789

Gnomad4 AMR exome

AF:

0.179

Gnomad4 ASJ exome

AF:

0.164

Gnomad4 EAS exome

AF:

0.253

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.134

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.140

AC:

21278

AN:

152194

Hom.:

1633

Cov.:

AF XY:

0.141

AC XY:

10484

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0843

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.296

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.131

Gnomad4 NFE

AF:

0.152

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.150

Hom.:

4709

Bravo

AF:

0.139

TwinsUK

AF:

0.152

AC:

565

ALSPAC

AF:

0.156

AC:

602

ESP6500AA

AF:

0.0876

AC:

386

ESP6500EA

AF:

0.152

AC:

1305

ExAC

AF:

0.165

AC:

19991

Asia WGS

AF:

0.226

AC:

787

AN:

3478

EpiCase

AF:

0.148

EpiControl

AF:

0.157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.20

T;T

Eigen

Benign

0.11

Eigen_PC

Benign

0.12

FATHMM_MKL

Uncertain

0.95

MetaRNN

Benign

0.0036

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

L;L

MutationTaster

Benign

0.089

P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.55

.;N

REVEL

Benign

0.090

Sift

Benign

0.099

.;T

Sift4G

Benign

0.23

T;T

Polyphen

0.89

P;P

Vest4

0.077

MPC

0.078

ClinPred

0.030

GERP RS

4.0

Varity_R

0.052

gMVP

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over