11-45805813-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_018389.5(SLC35C1):c.12C>T(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC35C1
NM_018389.5 synonymous
NM_018389.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.383
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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 11-45805813-C-T is Benign according to our data. Variant chr11-45805813-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3010683.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.383 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SLC35C1 | NM_018389.5 | c.12C>T | p.Ala4= | synonymous_variant | 1/2 | ENST00000314134.4 | |
| SLC35C1 | XM_011520203.4 | c.12C>T | p.Ala4= | synonymous_variant | 1/2 | ||
| SLC35C1 | NM_001145265.2 | c.-28C>T | 5_prime_UTR_variant | 2/3 | |||
| SLC35C1 | NM_001145266.1 | c.-28C>T | 5_prime_UTR_variant | 2/3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC35C1 | ENST00000314134.4 | c.12C>T | p.Ala4= | synonymous_variant | 1/2 | 1 | NM_018389.5 | P4 | |
| SLC35C1 | ENST00000442528.2 | c.-28C>T | 5_prime_UTR_variant | 2/3 | 1 | A1 | |||
| SLC35C1 | ENST00000526817.2 | c.-28C>T | 5_prime_UTR_variant | 2/3 | 2 | A1 | |||
| SLC35C1 | ENST00000530471.1 | c.-28C>T | 5_prime_UTR_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461326Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 726960
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
1461326
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Cov.:
35
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0
AN XY:
726960
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
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 | Labcorp Genetics (formerly Invitae), Labcorp | Apr 08, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
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