chr12-10123373-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_197947.3(CLEC7A):c.493-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,344,770 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 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000092 ( 0 hom. )
Consequence
CLEC7A
NM_197947.3 splice_polypyrimidine_tract, intron
NM_197947.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00005226
2
Clinical Significance
Conservation
PhyloP100: 2.51
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 -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 12-10123373-A-G is Benign according to our data. Variant chr12-10123373-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3035819.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.493-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000304084.13 | |||
LOC105369655 | XR_007063208.1 | n.182-7708A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.493-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000594 AC: 9AN: 151398Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249420Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134958
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GnomAD4 exome AF: 0.00000922 AC: 11AN: 1193372Hom.: 0 Cov.: 18 AF XY: 0.00000329 AC XY: 2AN XY: 607414
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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 | Aug 09, 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
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at