dbSNP rs7173860: SLC28A1:c.-132-362A>C (chr15-84886310-A-C) – 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.-132-362A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 984,476 control chromosomes in the GnomAD database, including 83,613 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 0.43 ( 14005 hom., cov: 32)

Exomes 𝑓: 0.41 ( 69608 hom. )

Consequence

SLC28A1
NM_004213.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.367

Publications

2 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:

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5 link	c.-132-362A>C		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.-132-362A>C	intron_variant	Intron 1 of 18	1	NM_004213.5	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3 link	c.-16-1435A>C	intron_variant	Intron 1 of 17	1		ENSP00000286749.3	O00337-1
SLC28A1	ENST00000338602.6 link	c.-132-362A>C	intron_variant	Intron 1 of 6	1		ENSP00000341629.2	O00337-2
SLC28A1	ENST00000538177.5 link	c.-16-1435A>C	intron_variant	Intron 1 of 14	2		ENSP00000443752.1	B7Z3L6

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64690

AN:

151760

Hom.:

14001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.487

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.404

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.428

GnomAD4 exome

AF:

0.409

AC:

340361

AN:

832600

Hom.:

69608

Cov.:

AF XY:

0.409

AC XY:

157251

AN XY:

384490

show subpopulations

African (AFR)

AF:

0.470

AC:

7423

AN:

15778

American (AMR)

AF:

0.359

AC:

353

AN:

982

Ashkenazi Jewish (ASJ)

AF:

0.485

AC:

2498

AN:

5146

East Asian (EAS)

AF:

0.496

AC:

1800

AN:

3630

South Asian (SAS)

AF:

0.337

AC:

5540

AN:

16444

European-Finnish (FIN)

AF:

0.442

AC:

122

AN:

276

Middle Eastern (MID)

AF:

0.381

AC:

618

AN:

1620

European-Non Finnish (NFE)

AF:

0.408

AC:

310658

AN:

761454

Other (OTH)

AF:

0.416

AC:

11349

AN:

27270

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

9516

19032

28549

38065

47581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13190

26380

39570

52760

65950

<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:

0.426

AC:

64726

AN:

151876

Hom.:

14005

Cov.:

AF XY:

0.424

AC XY:

31454

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.461

AC:

19079

AN:

41398

American (AMR)

AF:

0.392

AC:

5984

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.487

AC:

1686

AN:

3464

East Asian (EAS)

AF:

0.485

AC:

2497

AN:

5148

South Asian (SAS)

AF:

0.329

AC:

1584

AN:

4812

European-Finnish (FIN)

AF:

0.405

AC:

4260

AN:

10530

Middle Eastern (MID)

AF:

0.390

AC:

114

AN:

292

European-Non Finnish (NFE)

AF:

0.414

AC:

28163

AN:

67960

Other (OTH)

AF:

0.425

AC:

895

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1885

3771

5656

7542

9427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.414

Hom.:

21306

Bravo

AF:

0.430

Asia WGS

AF:

0.420

AC:

1459

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

(source)

DANN

Benign

0.49

PhyloP100

-0.37

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over