rs1060896

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004212.4(SLC28A2):c.225C>A(p.Ser75Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 1,610,694 control chromosomes in the GnomAD database, including 308,023 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 20716 hom., cov: 31)

Exomes 𝑓: 0.61 ( 287307 hom. )

Consequence

SLC28A2
NM_004212.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.37

Publications

56 publications found

Variant links:

Genes affected

SLC28A2 (HGNC:11002): (solute carrier family 28 member 2) Enables neurotransmitter transmembrane transporter activity and nucleoside transmembrane transporter activity. Involved in several processes, including nucleoside transport; purine nucleobase transmembrane transport; and pyrimidine-containing compound transmembrane transport. Predicted to be located in membrane. Predicted to be part of brush border membrane; coated vesicle; and vesicle membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC28A2 links:

SLC28A2-AS1 (HGNC:55417): (SLC28A2 antisense RNA 1)

SLC28A2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.6951517E-6).

BP6

Variant 15-45262069-C-A is Benign according to our data. Variant chr15-45262069-C-A is described in ClinVar as [Benign]. Clinvar id is 1267759.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A2	NM_004212.4 link	c.225C>A	p.Ser75Arg	missense_variant	Exon 4 of 18	ENST00000347644.8	NP_004203.2	O43868Q2M2A7Q53H72
SLC28A2-AS1	NR_120335.1 link	n.27-6071G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A2	ENST00000347644.8 link	c.225C>A	p.Ser75Arg	missense_variant	Exon 4 of 18	1	NM_004212.4	ENSP00000315006.4		O43868

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71905

AN:

151958

Hom.:

20722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.748

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.0958

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.490

GnomAD2 exomes

AF:

0.501

AC:

125660

AN:

251060

AF XY:

0.518

show subpopulations

Gnomad AFR exome

AF:

0.173

Gnomad AMR exome

AF:

0.300

Gnomad ASJ exome

AF:

0.584

Gnomad EAS exome

AF:

0.0855

Gnomad FIN exome

AF:

0.592

Gnomad NFE exome

AF:

0.653

Gnomad OTH exome

AF:

0.561

GnomAD4 exome

AF:

0.611

AC:

890706

AN:

1458618

Hom.:

287307

Cov.:

AF XY:

0.610

AC XY:

442642

AN XY:

725744

show subpopulations

African (AFR)

AF:

0.162

AC:

5416

AN:

33416

American (AMR)

AF:

0.317

AC:

14142

AN:

44660

Ashkenazi Jewish (ASJ)

AF:

0.585

AC:

15254

AN:

26078

East Asian (EAS)

AF:

0.0665

AC:

2639

AN:

39684

South Asian (SAS)

AF:

0.487

AC:

41930

AN:

86078

European-Finnish (FIN)

AF:

0.597

AC:

31878

AN:

53380

Middle Eastern (MID)

AF:

0.523

AC:

3014

AN:

5762

European-Non Finnish (NFE)

AF:

0.669

AC:

741946

AN:

1109314

Other (OTH)

AF:

0.572

AC:

34487

AN:

60246

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

14831

29661

44492

59322

74153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.473

AC:

71898

AN:

152076

Hom.:

20716

Cov.:

AF XY:

0.464

AC XY:

34527

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.182

AC:

7541

AN:

41476

American (AMR)

AF:

0.408

AC:

6230

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.581

AC:

2014

AN:

3468

East Asian (EAS)

AF:

0.0956

AC:

495

AN:

5178

South Asian (SAS)

AF:

0.452

AC:

2178

AN:

4816

European-Finnish (FIN)

AF:

0.601

AC:

6348

AN:

10556

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

45238

AN:

67986

Other (OTH)

AF:

0.485

AC:

1024

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1563

3126

4689

6252

7815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.559

Hom.:

48463

Bravo

AF:

0.443

TwinsUK

AF:

0.672

AC:

2493

ALSPAC

AF:

0.663

AC:

2555

ESP6500AA

AF:

0.196

AC:

861

ESP6500EA

AF:

0.665

AC:

5714

ExAC

AF:

0.502

AC:

60912

Asia WGS

AF:

0.279

AC:

971

AN:

3478

EpiCase

AF:

0.654

EpiControl

AF:

0.651

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jan 18, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 30315176) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.36

CADD

Benign

0.21

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.0067

T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.11

T;T

MetaRNN

Benign

0.0000057

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.26

N;.

PhyloP100

-1.4

PrimateAI

Benign

0.21

PROVEAN

Benign

0.28

N;N

REVEL

Uncertain

0.35

Sift

Benign

0.56

T;T

Sift4G

Benign

0.50

T;T

Polyphen

0.0

B;.

Vest4

0.050

MutPred

0.16

Gain of MoRF binding (P = 0.0107);.;

MPC

0.044

ClinPred

0.0013

GERP RS

-3.7

Varity_R

0.052

gMVP

0.13

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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rs1060896

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over