dbSNP rs2413775: SLC28A2-AS1:n.1963A>T (chr15-45252090-T-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000560344.6(SLC28A2-AS1):n.1963A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 424,826 control chromosomes in the GnomAD database, including 83,943 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 0.61 ( 29256 hom., cov: 33)

Exomes 𝑓: 0.62 ( 54687 hom. )

Consequence

SLC28A2-AS1
ENST00000560344.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

9 publications found

Variant links:

COSMIC-nc: COSV61665430

Genes affected

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

SLC28A2-AS1 links:

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560344.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A2-AS1	NR_120335.1		n.181-18A>T		intron	N/A
	SLC28A2	NM_004212.4	MANE Select	c.-205T>A		upstream_gene	N/A	NP_004203.2	O43868

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SLC28A2-AS1	ENST00000560344.6	TSL:5	n.1963A>T	non_coding_transcript_exon	Exon 4 of 4
SLC28A2-AS1	ENST00000559003.5	TSL:2	n.244-18A>T	intron	N/A
SLC28A2-AS1	ENST00000663463.1		n.56-9560A>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.611

AC:

92865

AN:

152058

Hom.:

29246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.577

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.621

AC:

169201

AN:

272650

Hom.:

54687

Cov.:

AF XY:

0.620

AC XY:

97245

AN XY:

156944

show subpopulations

African (AFR)

AF:

0.564

AC:

3588

AN:

6362

American (AMR)

AF:

0.392

AC:

6552

AN:

16714

Ashkenazi Jewish (ASJ)

AF:

0.624

AC:

5815

AN:

9316

East Asian (EAS)

AF:

0.195

AC:

1766

AN:

9062

South Asian (SAS)

AF:

0.587

AC:

32098

AN:

54704

European-Finnish (FIN)

AF:

0.633

AC:

7744

AN:

12226

Middle Eastern (MID)

AF:

0.663

AC:

682

AN:

1028

European-Non Finnish (NFE)

AF:

0.684

AC:

102952

AN:

150442

Other (OTH)

AF:

0.626

AC:

8004

AN:

12796

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3146

6293

9439

12586

15732

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

392

784

1176

1568

1960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.610

AC:

92897

AN:

152176

Hom.:

29256

Cov.:

AF XY:

0.605

AC XY:

45044

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.577

AC:

23940

AN:

41516

American (AMR)

AF:

0.502

AC:

7670

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.617

AC:

2141

AN:

3472

East Asian (EAS)

AF:

0.193

AC:

1001

AN:

5184

South Asian (SAS)

AF:

0.570

AC:

2745

AN:

4814

European-Finnish (FIN)

AF:

0.631

AC:

6673

AN:

10578

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.685

AC:

46559

AN:

68006

Other (OTH)

AF:

0.598

AC:

1264

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1844

3689

5533

7378

9222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.632

Hom.:

3832

Bravo

AF:

0.596

Asia WGS

AF:

0.395

AC:

1378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

1.2

PromoterAI

-0.0025

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over