Variant rs2242047 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004213.5(SLC28A1):c.1528C>T(p.Arg510Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0351 in 1,614,108 control chromosomes in the GnomAD database, including 3,993 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.051 ( 534 hom., cov: 32)

Exomes 𝑓: 0.033 ( 3459 hom. )

Consequence

SLC28A1
NM_004213.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 3.75

Variant links:

Genes affected

SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC28A1 links:

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 (MetaRNN=0.0031405985).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A1	NM_004213.5 linkuse as main transcript	c.1528C>T	p.Arg510Cys	missense_variant	15/19	ENST00000394573.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A1	ENST00000394573.6 linkuse as main transcript	c.1528C>T	p.Arg510Cys	missense_variant	15/19	1	NM_004213.5	P1	O00337-1
SLC28A1	ENST00000286749.3 linkuse as main transcript	c.1528C>T	p.Arg510Cys	missense_variant	14/18	1		P1	O00337-1
SLC28A1	ENST00000538177.5 linkuse as main transcript	c.1084-7980C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0510

AC:

7766

AN:

152168

Hom.:

536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0294

Gnomad ASJ

AF:

0.0657

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.0931

Gnomad FIN

AF:

0.0165

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0493

GnomAD3 exomes

AF:

0.0583

AC:

14656

AN:

251410

Hom.:

1460

AF XY:

0.0580

AC XY:

7885

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.0811

Gnomad AMR exome

AF:

0.0216

Gnomad ASJ exome

AF:

0.0652

Gnomad EAS exome

AF:

0.360

Gnomad SAS exome

AF:

0.0938

Gnomad FIN exome

AF:

0.0142

Gnomad NFE exome

AF:

0.0160

Gnomad OTH exome

AF:

0.0505

GnomAD4 exome

AF:

0.0334

AC:

48872

AN:

1461822

Hom.:

3459

Cov.:

AF XY:

0.0347

AC XY:

25260

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.0800

Gnomad4 AMR exome

AF:

0.0231

Gnomad4 ASJ exome

AF:

0.0617

Gnomad4 EAS exome

AF:

0.350

Gnomad4 SAS exome

AF:

0.0916

Gnomad4 FIN exome

AF:

0.0128

Gnomad4 NFE exome

AF:

0.0159

Gnomad4 OTH exome

AF:

0.0516

GnomAD4 genome

AF:

0.0510

AC:

7770

AN:

152286

Hom.:

534

Cov.:

AF XY:

0.0538

AC XY:

4008

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0831

Gnomad4 AMR

AF:

0.0293

Gnomad4 ASJ

AF:

0.0657

Gnomad4 EAS

AF:

0.357

Gnomad4 SAS

AF:

0.0935

Gnomad4 FIN

AF:

0.0165

Gnomad4 NFE

AF:

0.0152

Gnomad4 OTH

AF:

0.0483

Alfa

AF:

0.0249

Hom.:

222

Bravo

AF:

0.0536

TwinsUK

AF:

0.0151

AC:

ALSPAC

AF:

0.0127

AC:

ESP6500AA

AF:

0.0853

AC:

376

ESP6500EA

AF:

0.0174

AC:

150

ExAC

AF:

0.0590

AC:

7159

Asia WGS

AF:

0.204

AC:

710

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SLC28A1-related condition

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 28, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Uridine-cytidineuria

Other:1

Affects, no assertion criteria provided

literature only

OMIM

Aug 06, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

Cadd

Pathogenic

Dann

Pathogenic

1.0

DEOGEN2

Benign

0.096

T;T

Eigen

Uncertain

0.48

Eigen_PC

Uncertain

0.44

FATHMM_MKL

Benign

0.58

LIST_S2

Benign

0.16

T;.

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Uncertain

2.3

M;M

MutationTaster

Benign

0.029

P;P;P;P;P

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-3.4

D;D

REVEL

Benign

0.12

Sift

Uncertain

0.021

D;D

Sift4G

Uncertain

0.054

T;T

Polyphen

1.0

D;D

Vest4

0.17

MPC

0.51

ClinPred

0.035

GERP RS

4.1

Varity_R

0.14

gMVP

0.59

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over