rs12708716
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015226(CLEC16A):c.2116+24994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152022 control chromosomes in the gnomAD Genomes database, including 10591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 10591 hom., cov: 33)
Consequence
CLEC16A
NM_015226 intron
NM_015226 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0260
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC16A | NM_015226.3 | c.2116+24994A>G | intron_variant | ENST00000409790.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.2116+24994A>G | intron_variant | 5 | NM_015226.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.370 AC: 56261AN: 152022Hom.: 10591 Cov.: 33
GnomAD3 genomes
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56261
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152022
Hom.:
Cov.:
33
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Asia WGS
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1198
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at