chr11-45811143-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_018389.5(SLC35C1):c.903G>T(p.Thr301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000974 in 1,611,482 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T301T) has been classified as Uncertain significance.
Frequency
Consequence
NM_018389.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35C1 | NM_018389.5 | c.903G>T | p.Thr301= | synonymous_variant | 2/2 | ENST00000314134.4 | |
SLC35C1 | NM_001145265.2 | c.864G>T | p.Thr288= | synonymous_variant | 3/3 | ||
SLC35C1 | NM_001145266.1 | c.864G>T | p.Thr288= | synonymous_variant | 3/3 | ||
SLC35C1 | XM_011520202.3 | c.396G>T | p.Thr132= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35C1 | ENST00000314134.4 | c.903G>T | p.Thr301= | synonymous_variant | 2/2 | 1 | NM_018389.5 | P4 | |
SLC35C1 | ENST00000442528.2 | c.864G>T | p.Thr288= | synonymous_variant | 3/3 | 1 | A1 | ||
SLC35C1 | ENST00000526817.2 | c.864G>T | p.Thr288= | synonymous_variant | 3/3 | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 246882Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134156
GnomAD4 exome AF: 0.000101 AC: 147AN: 1459246Hom.: 0 Cov.: 36 AF XY: 0.000102 AC XY: 74AN XY: 726088
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74372
ClinVar
Submissions by phenotype
Leukocyte adhesion deficiency type II Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at