chr20-46724875-C-CGGATGGATGGATGGAT
Position:
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
NM_030777.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.234
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 20-46724875-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 |
---|---|---|---|---|---|---|---|
SLC2A10 | NM_030777.4 | c.5-151_5-136dup | intron_variant | ENST00000359271.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A10 | ENST00000359271.4 | c.5-151_5-136dup | intron_variant | 1 | NM_030777.4 | P1 | |||
SLC2A10 | ENST00000611837.1 | n.157-151_157-136dup | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0518 AC: 7228AN: 139616Hom.: 295 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0518 AC: 7243AN: 139732Hom.: 298 Cov.: 0 AF XY: 0.0519 AC XY: 3518AN XY: 67756
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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 submitter | clinical testing | GeneDx | Aug 10, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at