12-10052733-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207345.4(CLEC9A):c.46G>A(p.Ala16Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00531 in 1,613,728 control chromosomes in the GnomAD database, including 403 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 202 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 201 hom. )
Consequence
CLEC9A
NM_207345.4 missense
NM_207345.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -2.36
Genes affected
CLEC9A (HGNC:26705): (C-type lectin domain containing 9A) CLEC9A is a group V C-type lectin-like receptor (CTLR) that functions as an activation receptor and is expressed on myeloid lineage cells (Huysamen et al., 2008 [PubMed 18408006]).[supplied by OMIM, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0014681816).
BP6
Variant 12-10052733-G-A is Benign according to our data. Variant chr12-10052733-G-A is described in ClinVar as [Benign]. Clinvar id is 768515.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC9A | NM_207345.4 | c.46G>A | p.Ala16Thr | missense_variant | 4/9 | ENST00000355819.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC9A | ENST00000355819.6 | c.46G>A | p.Ala16Thr | missense_variant | 4/9 | 1 | NM_207345.4 | P1 | |
CLEC9A | ENST00000544751.1 | n.1193G>A | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0282 AC: 4280AN: 151972Hom.: 200 Cov.: 32
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GnomAD3 exomes AF: 0.00730 AC: 1836AN: 251434Hom.: 87 AF XY: 0.00573 AC XY: 779AN XY: 135894
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GnomAD4 exome AF: 0.00293 AC: 4281AN: 1461666Hom.: 201 Cov.: 31 AF XY: 0.00246 AC XY: 1791AN XY: 727136
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GnomAD4 genome AF: 0.0282 AC: 4284AN: 152062Hom.: 202 Cov.: 32 AF XY: 0.0273 AC XY: 2030AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 04, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
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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