12-8520253-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_080387.5(CLEC4D):c.412C>T(p.Arg138Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,782 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 (★).
Frequency
Consequence
NM_080387.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLEC4D | NM_080387.5 | c.412C>T | p.Arg138Trp | missense_variant | Exon 5 of 6 | ENST00000299665.3 | NP_525126.2 | |
CLEC4D | XM_011520632.3 | c.412C>T | p.Arg138Trp | missense_variant | Exon 6 of 7 | XP_011518934.1 | ||
CLEC4D | XM_047428771.1 | c.384+1093C>T | intron_variant | Intron 4 of 5 | XP_047284727.1 | |||
CLEC4D | XM_047428772.1 | c.384+1093C>T | intron_variant | Intron 4 of 5 | XP_047284728.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251438Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135894
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461622Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727124
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.412C>T (p.R138W) alteration is located in exon 5 (coding exon 5) of the CLEC4D gene. This alteration results from a C to T substitution at nucleotide position 412, causing the arginine (R) at amino acid position 138 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at