Genetic Variant SLC28A2-AS1:n.1932A>C (chr15-45252121-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000560344.6(SLC28A2-AS1):n.1932A>C 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 0.984 in 449,966 control chromosomes in the GnomAD database, including 218,045 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 0.98 ( 73733 hom., cov: 32)

Exomes 𝑓: 0.98 ( 144312 hom. )

Consequence

SLC28A2-AS1
ENST00000560344.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.310

Publications

1 publications found

Variant links:

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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.181-49A>C		intron	N/A
	SLC28A2	NM_004212.4	MANE Select	c.-174T>G		upstream_gene	N/A	NP_004203.2	O43868

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SLC28A2-AS1	ENST00000560344.6	TSL:5	n.1932A>C	non_coding_transcript_exon	Exon 4 of 4
SLC28A2-AS1	ENST00000559003.5	TSL:2	n.244-49A>C	intron	N/A
SLC28A2-AS1	ENST00000663463.1		n.56-9591A>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.983

AC:

149668

AN:

152226

Hom.:

73680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.985

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.968

Gnomad ASJ

AF:

0.981

Gnomad EAS

AF:

0.787

Gnomad SAS

AF:

0.988

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.998

Gnomad OTH

AF:

0.982

GnomAD4 exome

AF:

0.984

AC:

292841

AN:

297622

Hom.:

144312

Cov.:

AF XY:

0.985

AC XY:

167623

AN XY:

170152

show subpopulations

African (AFR)

AF:

0.981

AC:

8020

AN:

8172

American (AMR)

AF:

0.949

AC:

24028

AN:

25314

Ashkenazi Jewish (ASJ)

AF:

0.981

AC:

10385

AN:

10590

East Asian (EAS)

AF:

0.795

AC:

7300

AN:

9188

South Asian (SAS)

AF:

0.991

AC:

58690

AN:

59200

European-Finnish (FIN)

AF:

0.998

AC:

12333

AN:

12354

Middle Eastern (MID)

AF:

0.991

AC:

1098

AN:

1108

European-Non Finnish (NFE)

AF:

0.997

AC:

157382

AN:

157818

Other (OTH)

AF:

0.980

AC:

13605

AN:

13878

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

236

472

707

943

1179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.983

AC:

149779

AN:

152344

Hom.:

73733

Cov.:

AF XY:

0.982

AC XY:

73158

AN XY:

74508

show subpopulations

African (AFR)

AF:

0.985

AC:

40948

AN:

41578

American (AMR)

AF:

0.968

AC:

14807

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.981

AC:

3406

AN:

3472

East Asian (EAS)

AF:

0.787

AC:

4074

AN:

5178

South Asian (SAS)

AF:

0.987

AC:

4769

AN:

4830

European-Finnish (FIN)

AF:

0.999

AC:

10614

AN:

10624

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.998

AC:

67888

AN:

68042

Other (OTH)

AF:

0.979

AC:

2072

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

117

234

352

469

586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

914

1828

2742

3656

4570

<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:

0.992

Hom.:

94606

Bravo

AF:

0.980

Asia WGS

AF:

0.893

AC:

3108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.1

(source)

DANN

Benign

0.72

PhyloP100

0.31

PromoterAI

0.059

Neutral

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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