chr20-46724806-AGGAT-A

Variant summary

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

The NM_030777.4(SLC2A10):​c.5-196_5-193del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 125,634 control chromosomes in the GnomAD database, including 92 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 92 hom., cov: 26)

Consequence

SLC2A10
NM_030777.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 20-46724806-AGGAT-A is Benign according to our data. Variant chr20-46724806-AGGAT-A is described in ClinVar as [Benign]. Clinvar id is 1270430.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC2A10NM_030777.4 linkuse as main transcriptc.5-196_5-193del intron_variant ENST00000359271.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC2A10ENST00000359271.4 linkuse as main transcriptc.5-196_5-193del intron_variant 1 NM_030777.4 P1
SLC2A10ENST00000611837.1 linkuse as main transcriptn.157-196_157-193del intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0306
AC:
3838
AN:
125508
Hom.:
92
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.0691
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.0179
Gnomad ASJ
AF:
0.0261
Gnomad EAS
AF:
0.0197
Gnomad SAS
AF:
0.0178
Gnomad FIN
AF:
0.0359
Gnomad MID
AF:
0.0388
Gnomad NFE
AF:
0.0137
Gnomad OTH
AF:
0.0244
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0306
AC:
3846
AN:
125634
Hom.:
92
Cov.:
26
AF XY:
0.0307
AC XY:
1862
AN XY:
60746
show subpopulations
Gnomad4 AFR
AF:
0.0692
Gnomad4 AMR
AF:
0.0178
Gnomad4 ASJ
AF:
0.0261
Gnomad4 EAS
AF:
0.0200
Gnomad4 SAS
AF:
0.0181
Gnomad4 FIN
AF:
0.0359
Gnomad4 NFE
AF:
0.0137
Gnomad4 OTH
AF:
0.0240

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 06, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

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

Other links and lift over

dbSNP: rs111504264; hg19: chr20-45353445; API