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.

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	UniProt
SLC28A1	NM_004213.5	MANE Select	c.-132-362A>C	intron	N/A	NP_004204.3
SLC28A1	NM_001287762.2		c.-16-1435A>C	intron	N/A	NP_001274691.1	O00337-1
SLC28A1	NM_001321722.2		c.-132-362A>C	intron	N/A	NP_001308651.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.-132-362A>C	intron	N/A	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3	TSL:1	c.-16-1435A>C	intron	N/A	ENSP00000286749.3	O00337-1
SLC28A1	ENST00000338602.6	TSL:1	c.-132-362A>C	intron	N/A	ENSP00000341629.2	O00337-2

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 v4.9

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

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