rs13125209
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020041.3(SLC2A9):c.681+172T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,106 control chromosomes in the GnomAD database, including 40,338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.72 ( 40338 hom., cov: 33)
Consequence
SLC2A9
NM_020041.3 intron
NM_020041.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.240
Genes affected
SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 4-9980420-A-C is Benign according to our data. Variant chr4-9980420-A-C is described in ClinVar as [Benign]. Clinvar id is 1295132.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A9 | NM_020041.3 | c.681+172T>G | intron_variant | ENST00000264784.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A9 | ENST00000264784.8 | c.681+172T>G | intron_variant | 1 | NM_020041.3 | A2 | |||
SLC2A9 | ENST00000309065.7 | c.594+172T>G | intron_variant | 1 | P2 | ||||
SLC2A9 | ENST00000505104.5 | n.715+172T>G | intron_variant, non_coding_transcript_variant | 1 | |||||
SLC2A9 | ENST00000506583.5 | c.594+172T>G | intron_variant | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.719 AC: 109234AN: 151988Hom.: 40331 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.718 AC: 109274AN: 152106Hom.: 40338 Cov.: 33 AF XY: 0.720 AC XY: 53577AN XY: 74370
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74370
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2921
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3478
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 | Nov 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at