dbSNP rs12909280: SLC28A1:c.-132-547T>G (chr15-84886125-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 NM_004213.5(SLC28A1):c.-132-547T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 984,082 control chromosomes in the GnomAD database, including 22,394 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 0.17 ( 2775 hom., cov: 32)

Exomes 𝑓: 0.21 ( 19619 hom. )

Consequence

SLC28A1
NM_004213.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

4 publications found

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:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004213.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC28A1	NM_004213.5	MANE Select	c.-132-547T>G	intron	N/A	NP_004204.3
SLC28A1	NM_001287762.2		c.-17+1374T>G	intron	N/A	NP_001274691.1
SLC28A1	NM_001321722.2		c.-132-547T>G	intron	N/A	NP_001308651.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.-132-547T>G	intron	N/A	ENSP00000378074.1
SLC28A1	ENST00000286749.3	TSL:1	c.-17+1374T>G	intron	N/A	ENSP00000286749.3
SLC28A1	ENST00000338602.6	TSL:1	c.-132-547T>G	intron	N/A	ENSP00000341629.2

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25648

AN:

152086

Hom.:

2780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0401

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.184

GnomAD4 exome

AF:

0.214

AC:

178370

AN:

831878

Hom.:

19619

Cov.:

AF XY:

0.215

AC XY:

82604

AN XY:

384206

show subpopulations

African (AFR)

AF:

0.0261

AC:

412

AN:

15784

American (AMR)

AF:

0.207

AC:

204

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

1271

AN:

5138

East Asian (EAS)

AF:

0.119

AC:

433

AN:

3624

South Asian (SAS)

AF:

0.144

AC:

2364

AN:

16446

European-Finnish (FIN)

AF:

0.272

AC:

AN:

276

Middle Eastern (MID)

AF:

0.199

AC:

323

AN:

1620

European-Non Finnish (NFE)

AF:

0.221

AC:

167878

AN:

760748

Other (OTH)

AF:

0.198

AC:

5410

AN:

27258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

6348

12697

19045

25394

31742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7854

15708

23562

31416

39270

<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:

0.168

AC:

25635

AN:

152204

Hom.:

2775

Cov.:

AF XY:

0.168

AC XY:

12536

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0400

AC:

1663

AN:

41550

American (AMR)

AF:

0.202

AC:

3090

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

805

AN:

3470

East Asian (EAS)

AF:

0.121

AC:

628

AN:

5184

South Asian (SAS)

AF:

0.134

AC:

645

AN:

4826

European-Finnish (FIN)

AF:

0.254

AC:

2689

AN:

10570

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15469

AN:

67988

Other (OTH)

AF:

0.182

AC:

385

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1057

2113

3170

4226

5283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.189

Hom.:

609

Bravo

AF:

0.160

Asia WGS

AF:

0.121

AC:

421

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.8

(source)

DANN

Benign

0.66

PhyloP100

-0.047

Mutation Taster

=100/0

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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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