1-9010137-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_207420.3(SLC2A7):c.1116+6A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000506 in 1,551,120 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00053 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00050 ( 1 hom. )
Consequence
SLC2A7
NM_207420.3 splice_donor_region, intron
NM_207420.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00001546
2
Clinical Significance
Conservation
PhyloP100: -0.142
Genes affected
SLC2A7 (HGNC:13445): (solute carrier family 2 member 7) SLC2A7 belongs to a family of transporters that catalyze the uptake of sugars through facilitated diffusion (Li et al., 2004). This family of transporters shows conservation of 12 transmembrane helices as well as functionally significant amino acid residues (Joost and Thorens, 2001 [PubMed 11780753]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 1-9010137-T-C is Benign according to our data. Variant chr1-9010137-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638182.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A7 | NM_207420.3 | c.1116+6A>G | splice_donor_region_variant, intron_variant | ENST00000400906.2 | |||
SLC2A7 | XM_011540824.3 | c.1116+6A>G | splice_donor_region_variant, intron_variant | ||||
SLC2A7 | XM_011540825.3 | c.1116+6A>G | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A7 | ENST00000400906.2 | c.1116+6A>G | splice_donor_region_variant, intron_variant | 1 | NM_207420.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000534 AC: 81AN: 151812Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000552 AC: 86AN: 155886Hom.: 0 AF XY: 0.000607 AC XY: 50AN XY: 82358
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GnomAD4 exome AF: 0.000503 AC: 704AN: 1399190Hom.: 1 Cov.: 33 AF XY: 0.000546 AC XY: 377AN XY: 690178
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GnomAD4 genome AF: 0.000533 AC: 81AN: 151930Hom.: 2 Cov.: 33 AF XY: 0.000512 AC XY: 38AN XY: 74272
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | SLC2A7: BP4 - |
Computational scores
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Name
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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