chr11-45805799-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000442528.2(SLC35C1):c.-31-11A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,612,660 control chromosomes in the GnomAD database, including 39,757 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.26 ( 6084 hom., cov: 32)
Exomes 𝑓: 0.21 ( 33673 hom. )
Consequence
SLC35C1
ENST00000442528.2 splice_polypyrimidine_tract, intron
ENST00000442528.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.745
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 11-45805799-A-G is Benign according to our data. Variant chr11-45805799-A-G is described in ClinVar as [Benign]. Clinvar id is 95903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35C1 | NM_018389.5 | c.-3A>G | 5_prime_UTR_variant | 1/2 | ENST00000314134.4 | NP_060859.4 | ||
SLC35C1 | XM_011520203.4 | c.-3A>G | 5_prime_UTR_variant | 1/2 | XP_011518505.1 | |||
SLC35C1 | NM_001145265.2 | c.-31-11A>G | splice_polypyrimidine_tract_variant, intron_variant | NP_001138737.1 | ||||
SLC35C1 | NM_001145266.1 | c.-31-11A>G | splice_polypyrimidine_tract_variant, intron_variant | NP_001138738.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC35C1 | ENST00000314134.4 | c.-3A>G | 5_prime_UTR_variant | 1/2 | 1 | NM_018389.5 | ENSP00000313318 | P4 | ||
SLC35C1 | ENST00000442528.2 | c.-31-11A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000412408 | A1 | ||||
SLC35C1 | ENST00000526817.2 | c.-31-11A>G | splice_polypyrimidine_tract_variant, intron_variant | 2 | ENSP00000432145 | A1 | ||||
SLC35C1 | ENST00000530471.1 | c.-31-11A>G | splice_polypyrimidine_tract_variant, intron_variant | 3 | ENSP00000432669 |
Frequencies
GnomAD3 genomes AF: 0.262 AC: 39871AN: 152020Hom.: 6070 Cov.: 32
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GnomAD3 exomes AF: 0.203 AC: 50541AN: 249226Hom.: 5889 AF XY: 0.198 AC XY: 26802AN XY: 135184
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GnomAD4 exome AF: 0.209 AC: 305644AN: 1460522Hom.: 33673 Cov.: 39 AF XY: 0.206 AC XY: 149905AN XY: 726548
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GnomAD4 genome AF: 0.262 AC: 39928AN: 152138Hom.: 6084 Cov.: 32 AF XY: 0.260 AC XY: 19366AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 20, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 04, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Leukocyte adhesion deficiency type II Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at