chr20-46709710-C-T
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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
NM_030777.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0300
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 -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 |
---|---|---|---|---|---|---|---|
SLC2A10 | NM_030777.4 | c.-27C>T | 5_prime_UTR_variant | 1/5 | ENST00000359271.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A10 | ENST00000359271.4 | c.-27C>T | 5_prime_UTR_variant | 1/5 | 1 | NM_030777.4 | P1 | ||
SLC2A10 | ENST00000486000.2 | c.-27C>T | 5_prime_UTR_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1935AN: 152110Hom.: 19 Cov.: 33
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GnomAD3 exomes AF: 0.0131 AC: 1732AN: 132646Hom.: 12 AF XY: 0.0129 AC XY: 929AN XY: 72196
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GnomAD4 exome AF: 0.0146 AC: 20302AN: 1389766Hom.: 168 Cov.: 30 AF XY: 0.0146 AC XY: 10016AN XY: 685488
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GnomAD4 genome AF: 0.0127 AC: 1934AN: 152222Hom.: 19 Cov.: 33 AF XY: 0.0135 AC XY: 1004AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2013 | This 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. - |
Arterial tortuosity syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This 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
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at