12-8520320-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_080387.5(CLEC4D):c.479C>T(p.Thr160Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000228 in 1,613,700 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 (★).
Frequency
Consequence
NM_080387.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLEC4D | NM_080387.5 | c.479C>T | p.Thr160Met | missense_variant | Exon 5 of 6 | ENST00000299665.3 | NP_525126.2 | |
CLEC4D | XM_011520632.3 | c.479C>T | p.Thr160Met | missense_variant | Exon 6 of 7 | XP_011518934.1 | ||
CLEC4D | XM_047428771.1 | c.384+1160C>T | intron_variant | Intron 4 of 5 | XP_047284727.1 | |||
CLEC4D | XM_047428772.1 | c.384+1160C>T | intron_variant | Intron 4 of 5 | XP_047284728.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251438Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135892
GnomAD4 exome AF: 0.000232 AC: 339AN: 1461598Hom.: 0 Cov.: 30 AF XY: 0.000228 AC XY: 166AN XY: 727108
GnomAD4 genome AF: 0.000191 AC: 29AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at