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
NM_030777.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00
Publications
0 publications found
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 syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P
- familial thoracic aortic aneurysm and aortic dissectionInheritance: AD Classification: LIMITED Submitted by: ClinGen
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00612 AC: 769AN: 125566Hom.: 6 Cov.: 26 show subpopulations
GnomAD3 genomes
AF:
AC:
769
AN:
125566
Hom.:
Cov.:
26
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00615 AC: 773AN: 125690Hom.: 6 Cov.: 26 AF XY: 0.00596 AC XY: 362AN XY: 60772 show subpopulations
GnomAD4 genome
AF:
AC:
773
AN:
125690
Hom.:
Cov.:
26
AF XY:
AC XY:
362
AN XY:
60772
show subpopulations
African (AFR)
AF:
AC:
402
AN:
32248
American (AMR)
AF:
AC:
34
AN:
12764
Ashkenazi Jewish (ASJ)
AF:
AC:
32
AN:
3218
East Asian (EAS)
AF:
AC:
104
AN:
3600
South Asian (SAS)
AF:
AC:
11
AN:
3318
European-Finnish (FIN)
AF:
AC:
3
AN:
7616
Middle Eastern (MID)
AF:
AC:
1
AN:
194
European-Non Finnish (NFE)
AF:
AC:
159
AN:
60172
Other (OTH)
AF:
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
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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