Genetic Variant SLC2A14:c.1072-91A>C (chr12-7818125-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 ENST00000431042.7(SLC2A14):c.1072-91A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,147,904 control chromosomes in the GnomAD database, including 184,365 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 0.51 ( 20545 hom., cov: 33)

Exomes 𝑓: 0.57 ( 163820 hom. )

Consequence

SLC2A14
ENST00000431042.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.485

Publications

9 publications found

Variant links:

Genes affected

SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]

SLC2A14 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431042.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC2A14	NM_001286234.2	MANE Select	c.1072-91A>C	intron	N/A	NP_001273163.1
SLC2A14	NM_001286237.2		c.1186-91A>C	intron	N/A	NP_001273166.1
SLC2A14	NM_001286233.2		c.1141-91A>C	intron	N/A	NP_001273162.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC2A14	ENST00000431042.7	TSL:1 MANE Select	c.1072-91A>C	intron	N/A	ENSP00000407287.2
SLC2A14	ENST00000396589.6	TSL:1	c.1141-91A>C	intron	N/A	ENSP00000379834.2
SLC2A14	ENST00000543909.5	TSL:1	c.1141-91A>C	intron	N/A	ENSP00000440480.1

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

78041

AN:

151982

Hom.:

20540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.428

Gnomad FIN

AF:

0.587

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.587

Gnomad OTH

AF:

0.530

GnomAD4 exome

AF:

0.569

AC:

566421

AN:

995804

Hom.:

163820

AF XY:

0.564

AC XY:

281510

AN XY:

499322

show subpopulations

African (AFR)

AF:

0.399

AC:

9083

AN:

22738

American (AMR)

AF:

0.418

AC:

9791

AN:

23448

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

9870

AN:

18196

East Asian (EAS)

AF:

0.401

AC:

14004

AN:

34920

South Asian (SAS)

AF:

0.437

AC:

26145

AN:

59882

European-Finnish (FIN)

AF:

0.599

AC:

28301

AN:

47230

Middle Eastern (MID)

AF:

0.468

AC:

2077

AN:

4442

European-Non Finnish (NFE)

AF:

0.597

AC:

442734

AN:

741012

Other (OTH)

AF:

0.556

AC:

24416

AN:

43936

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

11259

22517

33776

45034

56293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10804

21608

32412

43216

54020

<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:

0.513

AC:

78072

AN:

152100

Hom.:

20545

Cov.:

AF XY:

0.508

AC XY:

37784

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.417

AC:

17285

AN:

41490

American (AMR)

AF:

0.448

AC:

6838

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.531

AC:

1841

AN:

3468

East Asian (EAS)

AF:

0.421

AC:

2175

AN:

5168

South Asian (SAS)

AF:

0.427

AC:

2060

AN:

4820

European-Finnish (FIN)

AF:

0.587

AC:

6216

AN:

10582

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.587

AC:

39935

AN:

67984

Other (OTH)

AF:

0.534

AC:

1128

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1918

3836

5753

7671

9589

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.508

Hom.:

13951

Bravo

AF:

0.500

Asia WGS

AF:

0.497

AC:

1725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.64

(source)

DANN

Benign

0.39

PhyloP100

-0.48

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