Genetic Variant SLC28A1:c.96+57G>A (chr15-84887913-G-A) – 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.96+57G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,289,002 control chromosomes in the GnomAD database, including 28,445 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 ( 2703 hom., cov: 32)

Exomes 𝑓: 0.21 ( 25742 hom. )

Consequence

SLC28A1
NM_004213.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Publications

8 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5 link	c.96+57G>A		intron_variant	Intron 3 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.96+57G>A	intron_variant	Intron 3 of 18	1	NM_004213.5	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3 link	c.96+57G>A	intron_variant	Intron 2 of 17	1		ENSP00000286749.3	O00337-1
SLC28A1	ENST00000338602.6 link	c.96+57G>A	intron_variant	Intron 3 of 6	1		ENSP00000341629.2	O00337-2
SLC28A1	ENST00000538177.5 link	c.96+57G>A	intron_variant	Intron 2 of 14	2		ENSP00000443752.1	B7Z3L6

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25313

AN:

151974

Hom.:

2706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0398

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.208

AC:

236763

AN:

1136910

Hom.:

25742

AF XY:

0.208

AC XY:

120923

AN XY:

581458

show subpopulations

African (AFR)

AF:

0.0336

AC:

905

AN:

26944

American (AMR)

AF:

0.199

AC:

8769

AN:

44150

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

5641

AN:

24024

East Asian (EAS)

AF:

0.114

AC:

4356

AN:

38262

South Asian (SAS)

AF:

0.142

AC:

11285

AN:

79610

European-Finnish (FIN)

AF:

0.250

AC:

13277

AN:

53206

Middle Eastern (MID)

AF:

0.250

AC:

1267

AN:

5066

European-Non Finnish (NFE)

AF:

0.222

AC:

181546

AN:

816024

Other (OTH)

AF:

0.196

AC:

9717

AN:

49624

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9687

19374

29060

38747

48434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5260

10520

15780

21040

26300

<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:

0.166

AC:

25300

AN:

152092

Hom.:

2703

Cov.:

AF XY:

0.166

AC XY:

12358

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0398

AC:

1651

AN:

41530

American (AMR)

AF:

0.197

AC:

3017

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

800

AN:

3468

East Asian (EAS)

AF:

0.118

AC:

611

AN:

5164

South Asian (SAS)

AF:

0.124

AC:

600

AN:

4820

European-Finnish (FIN)

AF:

0.254

AC:

2683

AN:

10562

Middle Eastern (MID)

AF:

0.195

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.225

AC:

15296

AN:

67948

Other (OTH)

AF:

0.181

AC:

383

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1044

2089

3133

4178

5222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.203

Hom.:

9549

Bravo

AF:

0.158

Asia WGS

AF:

0.115

AC:

398

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.45

(source)

DANN

Benign

0.38

PhyloP100

-0.92

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