rs368103927
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_018389.5(SLC35C1):c.840C>A(p.Ile280=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,202 control chromosomes in the GnomAD database, including 2 homozygotes. 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. I280I) has been classified as Likely benign.
Frequency
Consequence
NM_018389.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35C1 | NM_018389.5 | c.840C>A | p.Ile280= | synonymous_variant | 2/2 | ENST00000314134.4 | |
SLC35C1 | NM_001145265.2 | c.801C>A | p.Ile267= | synonymous_variant | 3/3 | ||
SLC35C1 | NM_001145266.1 | c.801C>A | p.Ile267= | synonymous_variant | 3/3 | ||
SLC35C1 | XM_011520202.3 | c.333C>A | p.Ile111= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35C1 | ENST00000314134.4 | c.840C>A | p.Ile280= | synonymous_variant | 2/2 | 1 | NM_018389.5 | P4 | |
SLC35C1 | ENST00000442528.2 | c.801C>A | p.Ile267= | synonymous_variant | 3/3 | 1 | A1 | ||
SLC35C1 | ENST00000526817.2 | c.801C>A | p.Ile267= | synonymous_variant | 3/3 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152230Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250458Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135542
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460854Hom.: 1 Cov.: 36 AF XY: 0.0000165 AC XY: 12AN XY: 726796
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74500
ClinVar
Submissions by phenotype
Leukocyte adhesion deficiency type II Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at