rs16957976
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015226.3(CLEC16A):c.1866+122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 522,824 control chromosomes in the GnomAD database, including 3,313 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 0.12 ( 1139 hom., cov: 32)
Exomes 𝑓: 0.10 ( 2174 hom. )
Consequence
CLEC16A
NM_015226.3 intron
NM_015226.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.337
Genes affected
CLEC16A (HGNC:29013): (C-type lectin domain containing 16A) This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC16A | NM_015226.3 | c.1866+122T>C | intron_variant | ENST00000409790.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.1866+122T>C | intron_variant | 5 | NM_015226.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.120 AC: 18217AN: 152022Hom.: 1136 Cov.: 32
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GnomAD4 exome AF: 0.103 AC: 38281AN: 370684Hom.: 2174 Cov.: 6 AF XY: 0.102 AC XY: 19363AN XY: 190624
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GnomAD4 genome ? AF: 0.120 AC: 18234AN: 152140Hom.: 1139 Cov.: 32 AF XY: 0.119 AC XY: 8814AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at