chr12-10127760-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_197947.3(CLEC7A):c.189C>T(p.Val63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000214 in 1,588,038 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 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CLEC7A
NM_197947.3 synonymous
NM_197947.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.464
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 -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 12-10127760-G-A is Benign according to our data. Variant chr12-10127760-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 743394.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.464 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.189C>T | p.Val63= | synonymous_variant | 2/6 | ENST00000304084.13 | |
LOC105369655 | XR_007063208.1 | n.182-3321G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.189C>T | p.Val63= | synonymous_variant | 2/6 | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000925 AC: 2AN: 216254Hom.: 0 AF XY: 0.00000868 AC XY: 1AN XY: 115264
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GnomAD4 exome AF: 0.0000230 AC: 33AN: 1436030Hom.: 0 Cov.: 30 AF XY: 0.0000183 AC XY: 13AN XY: 711922
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: -13
Find out detailed SpliceAI scores and Pangolin per-transcript scores at