rs3931701
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006931.3(SLC2A3):c.1068+4G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.054 ( 552 hom., cov: 28)
Exomes 𝑓: 0.0060 ( 722 hom. )
Failed GnomAD Quality Control
Consequence
SLC2A3
NM_006931.3 splice_donor_region, intron
NM_006931.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00006109
2
Clinical Significance
Conservation
PhyloP100: 0.860
Genes affected
SLC2A3 (HGNC:11007): (solute carrier family 2 member 3) Enables dehydroascorbic acid transmembrane transporter activity; glucose binding activity; and glucose transmembrane transporter activity. Involved in glucose import across plasma membrane and transport across blood-brain barrier. Is integral component of plasma membrane. Biomarker of Alzheimer's disease; acanthosis nigricans; diabetes mellitus; and type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 12-7924406-C-T is Benign according to our data. Variant chr12-7924406-C-T is described in ClinVar as [Benign]. Clinvar id is 771454.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A3 | NM_006931.3 | c.1068+4G>A | splice_donor_region_variant, intron_variant | ENST00000075120.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A3 | ENST00000075120.12 | c.1068+4G>A | splice_donor_region_variant, intron_variant | 1 | NM_006931.3 | P1 | |||
SLC2A3 | ENST00000486749.5 | n.1809+4G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 1 | |||||
SLC2A3 | ENST00000707174.1 | c.1068+4G>A | splice_donor_region_variant, intron_variant | P1 | |||||
SLC2A3 | ENST00000479059.3 | n.579+4G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 8042AN: 150084Hom.: 552 Cov.: 28 FAILED QC
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GnomAD3 exomes AF: 0.0118 AC: 2906AN: 245340Hom.: 293 AF XY: 0.0105 AC XY: 1399AN XY: 132946
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00602 AC: 8714AN: 1446656Hom.: 722 Cov.: 31 AF XY: 0.00626 AC XY: 4506AN XY: 719504
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0536 AC: 8049AN: 150200Hom.: 552 Cov.: 28 AF XY: 0.0537 AC XY: 3940AN XY: 73384
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at