chr20-46724875-C-CGGATGGATGGATGGAT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030777.4(SLC2A10):​c.5-151_5-136dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 298 hom., cov: 0)

Consequence

SLC2A10
NM_030777.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.234
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 20-46724875-C-CGGATGGATGGATGGAT is Benign according to our data. Variant chr20-46724875-C-CGGATGGATGGATGGAT is described in ClinVar as [Benign]. Clinvar id is 1241818.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC2A10NM_030777.4 linkuse as main transcriptc.5-151_5-136dup intron_variant ENST00000359271.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC2A10ENST00000359271.4 linkuse as main transcriptc.5-151_5-136dup intron_variant 1 NM_030777.4 P1
SLC2A10ENST00000611837.1 linkuse as main transcriptn.157-151_157-136dup intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0518
AC:
7228
AN:
139616
Hom.:
295
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0753
Gnomad AMI
AF:
0.0359
Gnomad AMR
AF:
0.0270
Gnomad ASJ
AF:
0.0378
Gnomad EAS
AF:
0.0727
Gnomad SAS
AF:
0.111
Gnomad FIN
AF:
0.0536
Gnomad MID
AF:
0.0483
Gnomad NFE
AF:
0.0398
Gnomad OTH
AF:
0.0498
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0518
AC:
7243
AN:
139732
Hom.:
298
Cov.:
0
AF XY:
0.0519
AC XY:
3518
AN XY:
67756
show subpopulations
Gnomad4 AFR
AF:
0.0751
Gnomad4 AMR
AF:
0.0274
Gnomad4 ASJ
AF:
0.0378
Gnomad4 EAS
AF:
0.0729
Gnomad4 SAS
AF:
0.111
Gnomad4 FIN
AF:
0.0536
Gnomad4 NFE
AF:
0.0398
Gnomad4 OTH
AF:
0.0533

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 10, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3092014; hg19: chr20-45353514; API