chr12-10126562-T-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_197947.3(CLEC7A):c.340+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,601,196 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
Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
CLEC7A
NM_197947.3 intron
NM_197947.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.139
Genes affected
CLEC7A (HGNC:14558): (C-type lectin domain containing 7A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. The encoded glycoprotein is a small type II membrane receptor with an extracellular C-type lectin-like domain fold and a cytoplasmic domain with an immunoreceptor tyrosine-based activation motif. It functions as a pattern-recognition receptor that recognizes a variety of beta-1,3-linked and beta-1,6-linked glucans from fungi and plants, and in this way plays a role in innate immune response. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 12-10126562-T-C is Benign according to our data. Variant chr12-10126562-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3042662.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-10126562-T-C is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.340+9A>G | intron_variant | ENST00000304084.13 | |||
LOC105369655 | XR_007063208.1 | n.182-4519T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.340+9A>G | intron_variant | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152188Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000218 AC: 52AN: 238078Hom.: 0 AF XY: 0.000239 AC XY: 31AN XY: 129740
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GnomAD4 exome AF: 0.000173 AC: 251AN: 1448890Hom.: 0 Cov.: 31 AF XY: 0.000182 AC XY: 131AN XY: 720764
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GnomAD4 genome AF: 0.000236 AC: 36AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CLEC7A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at