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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5 link	c.-132-547T>G		intron_variant	Intron 1 of 18	ENST00000394573.6	NP_004204.3	O00337-1B7Z3L5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC28A1	ENST00000394573.6 link	c.-132-547T>G	intron_variant	Intron 1 of 18	1	NM_004213.5	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3 link	c.-17+1374T>G	intron_variant	Intron 1 of 17	1		ENSP00000286749.3	O00337-1
SLC28A1	ENST00000338602.6 link	c.-132-547T>G	intron_variant	Intron 1 of 6	1		ENSP00000341629.2	O00337-2
SLC28A1	ENST00000538177.5 link	c.-17+1374T>G	intron_variant	Intron 1 of 14	2		ENSP00000443752.1	B7Z3L6

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

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

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 v4.3

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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rs12909280

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over