chr6-87472986-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006416.5(SLC35A1):c.-18G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 657,550 control chromosomes in the GnomAD database, including 101,285 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 30014 hom., cov: 34)
Exomes 𝑓: 0.52 ( 71271 hom. )
Consequence
SLC35A1
NM_006416.5 5_prime_UTR
NM_006416.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.620
Genes affected
SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 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=-0.77).
BP6
?
Variant 6-87472986-G-C is Benign according to our data. Variant chr6-87472986-G-C is described in ClinVar as [Benign]. Clinvar id is 95391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A1 | NM_006416.5 | c.-18G>C | 5_prime_UTR_variant | 1/8 | ENST00000369552.9 | ||
SLC35A1 | NM_001168398.2 | c.-18G>C | 5_prime_UTR_variant | 1/7 | |||
LOC124901357 | XR_007059668.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A1 | ENST00000369552.9 | c.-18G>C | 5_prime_UTR_variant | 1/8 | 1 | NM_006416.5 | P1 | ||
SLC35A1 | ENST00000369556.7 | c.-18G>C | 5_prime_UTR_variant | 1/7 | 1 | ||||
SLC35A1 | ENST00000369557.9 | c.-18G>C | 5_prime_UTR_variant | 1/6 | 2 | ||||
SLC35A1 | ENST00000464978.5 | n.91+2273G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.615 AC: 93553AN: 152000Hom.: 29958 Cov.: 34
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GnomAD3 exomes AF: 0.598 AC: 7759AN: 12976Hom.: 2345 AF XY: 0.582 AC XY: 3758AN XY: 6454
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GnomAD4 exome AF: 0.525 AC: 265277AN: 505432Hom.: 71271 Cov.: 7 AF XY: 0.525 AC XY: 137165AN XY: 261452
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GnomAD4 genome ? AF: 0.616 AC: 93671AN: 152118Hom.: 30014 Cov.: 34 AF XY: 0.613 AC XY: 45548AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2015 | 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) | Jan 20, 2016 | - - |
SLC35A1-congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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