20-46724806-AGGATGGATGGATGGATGGAT-AGGATGGATGGATGGATGGATGGATGGAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_030777.4(SLC2A10):​c.5-200_5-193dupATGGATGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00615 in 125,690 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0062 ( 6 hom., cov: 26)

Consequence

SLC2A10
NM_030777.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

0 publications found
Variant links:
Genes affected
SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]
SLC2A10 Gene-Disease associations (from GenCC):
  • arterial tortuosity syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P
  • familial thoracic aortic aneurysm and aortic dissection
    Inheritance: AD Classification: LIMITED Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00615 (773/125690) while in subpopulation EAS AF = 0.0289 (104/3600). AF 95% confidence interval is 0.0244. There are 6 homozygotes in GnomAd4. There are 362 alleles in the male GnomAd4 subpopulation. Median coverage is 26. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 6 AR,AD gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A10NM_030777.4 linkc.5-200_5-193dupATGGATGG intron_variant Intron 1 of 4 ENST00000359271.4 NP_110404.1 O95528

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A10ENST00000359271.4 linkc.5-235_5-234insGGATGGAT intron_variant Intron 1 of 4 1 NM_030777.4 ENSP00000352216.2 O95528
SLC2A10ENST00000611837.1 linkn.157-235_157-234insGGATGGAT intron_variant Intron 1 of 1 2

Frequencies

GnomAD3 genomes
AF:
0.00612
AC:
769
AN:
125566
Hom.:
6
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.0124
Gnomad AMI
AF:
0.0221
Gnomad AMR
AF:
0.00267
Gnomad ASJ
AF:
0.00994
Gnomad EAS
AF:
0.0289
Gnomad SAS
AF:
0.00332
Gnomad FIN
AF:
0.000394
Gnomad MID
AF:
0.00485
Gnomad NFE
AF:
0.00266
Gnomad OTH
AF:
0.00510
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00615
AC:
773
AN:
125690
Hom.:
6
Cov.:
26
AF XY:
0.00596
AC XY:
362
AN XY:
60772
show subpopulations
African (AFR)
AF:
0.0125
AC:
402
AN:
32248
American (AMR)
AF:
0.00266
AC:
34
AN:
12764
Ashkenazi Jewish (ASJ)
AF:
0.00994
AC:
32
AN:
3218
East Asian (EAS)
AF:
0.0289
AC:
104
AN:
3600
South Asian (SAS)
AF:
0.00332
AC:
11
AN:
3318
European-Finnish (FIN)
AF:
0.000394
AC:
3
AN:
7616
Middle Eastern (MID)
AF:
0.00515
AC:
1
AN:
194
European-Non Finnish (NFE)
AF:
0.00264
AC:
159
AN:
60172
Other (OTH)
AF:
0.00559
AC:
10
AN:
1790
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
31
62
94
125
156
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
0.000374
Hom.:
16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.0
Mutation Taster
=100/0
polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs111504264; hg19: chr20-45353445; API