chr20-46709754-G-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_030777.4(SLC2A10):c.4+14G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,547,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000079 ( 0 hom. )
Consequence
SLC2A10
NM_030777.4 intron
NM_030777.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.57
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 20-46709754-G-C is Benign according to our data. Variant chr20-46709754-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2750114.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A10 | NM_030777.4 | c.4+14G>C | intron_variant | ENST00000359271.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A10 | ENST00000359271.4 | c.4+14G>C | intron_variant | 1 | NM_030777.4 | P1 | |||
SLC2A10 | ENST00000486000.2 | c.4+14G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152148Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000216 AC: 3AN: 139084Hom.: 0 AF XY: 0.0000265 AC XY: 2AN XY: 75376
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GnomAD4 exome AF: 0.00000788 AC: 11AN: 1395266Hom.: 0 Cov.: 31 AF XY: 0.00000726 AC XY: 5AN XY: 688248
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GnomAD4 genome AF: 0.0000986 AC: 15AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74322
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Arterial tortuosity syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2022 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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