chr11-45805249-A-AAGCCCCG
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018389.5(SLC35C1):c.-546_-540dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000077 in 973,788 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000081 ( 0 hom. )
Consequence
SLC35C1
NM_018389.5 5_prime_UTR
NM_018389.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -3.00
Genes affected
SLC35C1 (HGNC:20197): (solute carrier family 35 member C1) This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SLC35C1 | NM_018389.5 | c.-546_-540dup | 5_prime_UTR_variant | 1/2 | ENST00000314134.4 | ||
| SLC35C1 | XM_011520203.4 | c.-546_-540dup | 5_prime_UTR_variant | 1/2 | |||
| SLC35C1 | NM_001145265.2 | c.-31-554_-31-548dup | intron_variant | ||||
| SLC35C1 | NM_001145266.1 | c.-31-554_-31-548dup | intron_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC35C1 | ENST00000314134.4 | c.-546_-540dup | 5_prime_UTR_variant | 1/2 | 1 | NM_018389.5 | P4 | ||
| SLC35C1 | ENST00000442528.2 | c.-31-554_-31-548dup | intron_variant | 1 | A1 | ||||
| SLC35C1 | ENST00000530471.1 | c.-92_-86dup | 5_prime_UTR_variant | 1/2 | 3 | ||||
| SLC35C1 | ENST00000526817.2 | c.-31-554_-31-548dup | intron_variant | 2 | A1 |
Frequencies
GnomAD3 genomes 0.0000535 AC: 7AN: 130738Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000807 AC: 68AN: 843050Hom.: 0 Cov.: 30 AF XY: 0.0000820 AC XY: 32AN XY: 390258
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GnomAD4 genome 0.0000535 AC: 7AN: 130738Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 4AN XY: 63220
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital disorder of glycosylation Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at