Genetic Variant SLC2A1:c.18+6524G>A (chr1-42952110-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006516.4(SLC2A1):c.18+6524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 498,752 control chromosomes in the GnomAD database, including 2,722 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 0.088 ( 751 hom., cov: 32)

Exomes 𝑓: 0.10 ( 1971 hom. )

Consequence

SLC2A1
NM_006516.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.208

Publications

5 publications found

Variant links:

Genes affected

SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]

SLC2A1 links:

ATP6V0CP4 (HGNC:40002): (ATPase H+ transporting V0 subunit c pseudogene 4)

ATP6V0CP4 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=-0.59).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006516.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1	NM_006516.4	MANE Select	c.18+6524G>A		intron	N/A	NP_006507.2	P11166

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC2A1	ENST00000426263.10	TSL:1 MANE Select	c.18+6524G>A	intron	N/A	ENSP00000416293.2	P11166
SLC2A1	ENST00000889577.1		c.18+6524G>A	intron	N/A	ENSP00000559636.1
SLC2A1	ENST00000958848.1		c.18+6524G>A	intron	N/A	ENSP00000628907.1

Frequencies

GnomAD3 genomes

AF:

0.0875

AC:

13304

AN:

152058

Hom.:

748

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0334

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0986

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0778

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0966

Gnomad OTH

AF:

0.0903

GnomAD4 exome

AF:

0.101

AC:

35030

AN:

346576

Hom.:

1971

Cov.:

AF XY:

0.103

AC XY:

18453

AN XY:

179852

show subpopulations

African (AFR)

AF:

0.0335

AC:

336

AN:

10016

American (AMR)

AF:

0.167

AC:

1972

AN:

11788

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

1218

AN:

11484

East Asian (EAS)

AF:

0.133

AC:

3386

AN:

25532

South Asian (SAS)

AF:

0.131

AC:

3282

AN:

24984

European-Finnish (FIN)

AF:

0.0749

AC:

1903

AN:

25420

Middle Eastern (MID)

AF:

0.0860

AC:

179

AN:

2082

European-Non Finnish (NFE)

AF:

0.0965

AC:

20628

AN:

213790

Other (OTH)

AF:

0.0990

AC:

2126

AN:

21480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1386

2772

4157

5543

6929

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

256

384

512

640

<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:

0.0875

AC:

13316

AN:

152176

Hom.:

751

Cov.:

AF XY:

0.0903

AC XY:

6715

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0335

AC:

1390

AN:

41520

American (AMR)

AF:

0.167

AC:

2554

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0986

AC:

342

AN:

3470

East Asian (EAS)

AF:

0.122

AC:

631

AN:

5162

South Asian (SAS)

AF:

0.137

AC:

662

AN:

4818

European-Finnish (FIN)

AF:

0.0778

AC:

824

AN:

10596

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0966

AC:

6570

AN:

68010

Other (OTH)

AF:

0.0889

AC:

188

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

628

1256

1883

2511

3139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0978

Hom.:

270

Bravo

AF:

0.0904

Asia WGS

AF:

0.105

AC:

366

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

0.21

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=98/2

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