chr21-18090726-GAA-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000400131.5(CHODL):c.-44-165764_-44-165763del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0013 ( 2 hom., cov: 0)
Consequence
CHODL
ENST00000400131.5 intron
ENST00000400131.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.557
Genes affected
CHODL (HGNC:17807): (chondrolectin) This gene encodes a type I membrane protein with a carbohydrate recognition domain characteristic of C-type lectins in its extracellular portion. In other proteins, this domain is involved in endocytosis of glycoproteins and exogenous sugar-bearing pathogens. This protein localizes predominantly to the perinuclear region. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHODL | NM_001204175.2 | c.-44-165764_-44-165763del | intron_variant | ||||
CHODL | NM_001204176.2 | c.-45+62774_-45+62775del | intron_variant | ||||
CHODL | NM_001204177.2 | c.-44-165764_-44-165763del | intron_variant | ||||
CHODL | NM_001204178.2 | c.-45+62774_-45+62775del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000432412.1 | n.224+9205_224+9206del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00131 AC: 164AN: 125180Hom.: 2 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00131 AC: 164AN: 125164Hom.: 2 Cov.: 0 AF XY: 0.00172 AC XY: 102AN XY: 59460
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59460
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at