rs377098836
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_018389.5(SLC35C1):c.975G>A(p.Thr325=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000901 in 1,609,374 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000089 ( 1 hom. )
Consequence
SLC35C1
NM_018389.5 synonymous
NM_018389.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.05
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 11-45811215-G-A is Benign according to our data. Variant chr11-45811215-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 530700.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.05 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35C1 | NM_018389.5 | c.975G>A | p.Thr325= | synonymous_variant | 2/2 | ENST00000314134.4 | |
SLC35C1 | NM_001145265.2 | c.936G>A | p.Thr312= | synonymous_variant | 3/3 | ||
SLC35C1 | NM_001145266.1 | c.936G>A | p.Thr312= | synonymous_variant | 3/3 | ||
SLC35C1 | XM_011520202.3 | c.468G>A | p.Thr156= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35C1 | ENST00000314134.4 | c.975G>A | p.Thr325= | synonymous_variant | 2/2 | 1 | NM_018389.5 | P4 | |
SLC35C1 | ENST00000442528.2 | c.936G>A | p.Thr312= | synonymous_variant | 3/3 | 1 | A1 | ||
SLC35C1 | ENST00000526817.2 | c.936G>A | p.Thr312= | synonymous_variant | 3/3 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152248Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000885 AC: 22AN: 248724Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134748
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GnomAD4 exome AF: 0.0000892 AC: 130AN: 1457126Hom.: 1 Cov.: 36 AF XY: 0.0000759 AC XY: 55AN XY: 724354
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GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74376
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leukocyte adhesion deficiency type II Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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