rs7442295
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020041.3(SLC2A9):c.681+15836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,134 control chromosomes in the GnomAD database, including 6,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.27 ( 6441 hom., cov: 32)
Consequence
SLC2A9
NM_020041.3 intron
NM_020041.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.995
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A9 | NM_020041.3 | c.681+15836T>C | intron_variant | ENST00000264784.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A9 | ENST00000264784.8 | c.681+15836T>C | intron_variant | 1 | NM_020041.3 | A2 | |||
SLC2A9 | ENST00000309065.7 | c.594+15836T>C | intron_variant | 1 | P2 | ||||
SLC2A9 | ENST00000505104.5 | n.715+15836T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
SLC2A9 | ENST00000506583.5 | c.594+15836T>C | intron_variant | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.275 AC: 41739AN: 152016Hom.: 6429 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.275 AC: 41787AN: 152134Hom.: 6441 Cov.: 32 AF XY: 0.273 AC XY: 20336AN XY: 74388
GnomAD4 genome
?
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152134
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32
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20336
AN XY:
74388
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Asia WGS
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556
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3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Uric acid concentration, serum, quantitative trait locus 2 Other:1
association, no assertion criteria provided | literature only | OMIM | Apr 01, 2008 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
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