GeneBe

rs5842674

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000400131.5(CHODL):​c.-44-165782_-44-165771delAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

CHODL
ENST00000400131.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.852

Publications

0 publications found
Variant links:
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHODLNM_001204177.2 linkc.-44-165774_-44-165763delAAAAAAAAAAAA intron_variant Intron 1 of 4 NP_001191106.1
CHODLNM_001204178.2 linkc.-45+62764_-45+62775delAAAAAAAAAAAA intron_variant Intron 2 of 5 NP_001191107.1
CHODLNM_001204175.2 linkc.-44-165774_-44-165763delAAAAAAAAAAAA intron_variant Intron 1 of 5 NP_001191104.1
CHODLNM_001204176.2 linkc.-45+62764_-45+62775delAAAAAAAAAAAA intron_variant Intron 2 of 6 NP_001191105.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHODLENST00000400131.5 linkc.-44-165782_-44-165771delAAAAAAAAAAAA intron_variant Intron 1 of 4 1 ENSP00000382996.1
CHODLENST00000400135.5 linkc.-45+62756_-45+62767delAAAAAAAAAAAA intron_variant Intron 2 of 5 1 ENSP00000383001.1
CHODLENST00000400127.5 linkc.-45+62756_-45+62767delAAAAAAAAAAAA intron_variant Intron 2 of 6 1 ENSP00000382992.1

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463044; API