chr20-46709710-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_030777.4(SLC2A10):​c.-27C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0144 in 1,541,988 control chromosomes in the GnomAD database, including 187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 19 hom., cov: 33)
Exomes 𝑓: 0.015 ( 168 hom. )

Consequence

SLC2A10
NM_030777.4 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0300
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 20-46709710-C-T is Benign according to our data. Variant chr20-46709710-C-T is described in ClinVar as [Benign]. Clinvar id is 139184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-46709710-C-T is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0127 (1934/152222) while in subpopulation NFE AF= 0.0169 (1152/67966). AF 95% confidence interval is 0.0161. There are 19 homozygotes in gnomad4. There are 1004 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC2A10NM_030777.4 linkuse as main transcriptc.-27C>T 5_prime_UTR_variant 1/5 ENST00000359271.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC2A10ENST00000359271.4 linkuse as main transcriptc.-27C>T 5_prime_UTR_variant 1/51 NM_030777.4 P1
SLC2A10ENST00000486000.2 linkuse as main transcriptc.-27C>T 5_prime_UTR_variant 1/23

Frequencies

GnomAD3 genomes
AF:
0.0127
AC:
1935
AN:
152110
Hom.:
19
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00275
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.0122
Gnomad ASJ
AF:
0.00950
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00765
Gnomad FIN
AF:
0.0274
Gnomad MID
AF:
0.0510
Gnomad NFE
AF:
0.0169
Gnomad OTH
AF:
0.0144
GnomAD3 exomes
AF:
0.0131
AC:
1732
AN:
132646
Hom.:
12
AF XY:
0.0129
AC XY:
929
AN XY:
72196
show subpopulations
Gnomad AFR exome
AF:
0.00318
Gnomad AMR exome
AF:
0.0101
Gnomad ASJ exome
AF:
0.00855
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00731
Gnomad FIN exome
AF:
0.0281
Gnomad NFE exome
AF:
0.0166
Gnomad OTH exome
AF:
0.0172
GnomAD4 exome
AF:
0.0146
AC:
20302
AN:
1389766
Hom.:
168
Cov.:
30
AF XY:
0.0146
AC XY:
10016
AN XY:
685488
show subpopulations
Gnomad4 AFR exome
AF:
0.00423
Gnomad4 AMR exome
AF:
0.0102
Gnomad4 ASJ exome
AF:
0.00965
Gnomad4 EAS exome
AF:
0.0000286
Gnomad4 SAS exome
AF:
0.00759
Gnomad4 FIN exome
AF:
0.0262
Gnomad4 NFE exome
AF:
0.0157
Gnomad4 OTH exome
AF:
0.0134
GnomAD4 genome
AF:
0.0127
AC:
1934
AN:
152222
Hom.:
19
Cov.:
33
AF XY:
0.0135
AC XY:
1004
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.00279
Gnomad4 AMR
AF:
0.0122
Gnomad4 ASJ
AF:
0.00950
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00745
Gnomad4 FIN
AF:
0.0274
Gnomad4 NFE
AF:
0.0169
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.0140
Hom.:
6
Bravo
AF:
0.0113
Asia WGS
AF:
0.00347
AC:
12
AN:
3468

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxFeb 01, 2013This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Arterial tortuosity syndrome Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
14
DANN
Benign
0.95
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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: rs149481442; hg19: chr20-45338349; API