rs150743224
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_018389.5(SLC35C1):c.903G>A(p.Thr301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,611,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T301T) has been classified as Likely benign.
Frequency
Consequence
NM_018389.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35C1 | NM_018389.5 | c.903G>A | p.Thr301= | synonymous_variant | 2/2 | ENST00000314134.4 | |
SLC35C1 | NM_001145265.2 | c.864G>A | p.Thr288= | synonymous_variant | 3/3 | ||
SLC35C1 | NM_001145266.1 | c.864G>A | p.Thr288= | synonymous_variant | 3/3 | ||
SLC35C1 | XM_011520202.3 | c.396G>A | p.Thr132= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35C1 | ENST00000314134.4 | c.903G>A | p.Thr301= | synonymous_variant | 2/2 | 1 | NM_018389.5 | P4 | |
SLC35C1 | ENST00000442528.2 | c.864G>A | p.Thr288= | synonymous_variant | 3/3 | 1 | A1 | ||
SLC35C1 | ENST00000526817.2 | c.864G>A | p.Thr288= | synonymous_variant | 3/3 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246882Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134156
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1459248Hom.: 0 Cov.: 36 AF XY: 0.0000151 AC XY: 11AN XY: 726088
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
Leukocyte adhesion deficiency type II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 13, 2021 | This sequence change affects codon 301 of the SLC35C1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SLC35C1 protein. This variant is present in population databases (rs150743224, ExAC 0.003%). This variant has not been reported in the literature in individuals affected with SLC35C1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at