dbSNP rs710218: SLC2A1-DT:n.546+1970T>A (chr1-42961547-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000416689.3(SLC2A1-DT):n.546+1970T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,168 control chromosomes in the GnomAD database, including 13,422 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 0.37 ( 13414 hom., cov: 32)

Exomes 𝑓: 0.33 ( 8 hom. )

Consequence

SLC2A1-DT
ENST00000416689.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119

Publications

28 publications found

Variant links:

Genes affected

SLC2A1-DT (HGNC:44187): (SLC2A1 divergent transcript)

SLC2A1-DT links:

ENSG00000283973 (HGNC:):

ENSG00000283973 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 (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A1-DT	NR_033967.1 link	n.529+1970T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SLC2A1-DT	ENST00000416689.3 link	n.546+1970T>A	intron_variant	Intron 1 of 2	2
SLC2A1-DT	ENST00000431759.7 link	n.529+1970T>A	intron_variant	Intron 1 of 3	2
ENSG00000283973	ENST00000640236.1 link	n.68+177A>T	intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56465

AN:

151862

Hom.:

13371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.335

GnomAD4 exome

AF:

0.326

AC:

AN:

184

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

132

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.352

AC:

AN:

122

Other (OTH)

AF:

0.154

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.372

AC:

56579

AN:

151984

Hom.:

13414

Cov.:

AF XY:

0.373

AC XY:

27723

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.676

AC:

27996

AN:

41438

American (AMR)

AF:

0.363

AC:

5549

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

861

AN:

3470

East Asian (EAS)

AF:

0.339

AC:

1749

AN:

5152

South Asian (SAS)

AF:

0.317

AC:

1527

AN:

4820

European-Finnish (FIN)

AF:

0.252

AC:

2658

AN:

10568

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.225

AC:

15277

AN:

67946

Other (OTH)

AF:

0.336

AC:

709

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1576

3151

4727

6302

7878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.302

Hom.:

1088

Bravo

AF:

0.389

Asia WGS

AF:

0.385

AC:

1337

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

4.5

(source)

DANN

Benign

0.53

PhyloP100

0.12

Splicing

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