dbSNP rs5842674: CHODL:c.-44-165782_-44-165771delAAAAAAAAAAAA (chr21-18090726-GAAAAAAAAAAAA-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001204177.2(CHODL):c.-44-165774_-44-165763delAAAAAAAAAAAA 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: not found (cov: 0)

Consequence

CHODL
NM_001204177.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.852

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]

CHODL links:

ENSG00000227330 (HGNC:):

ENSG00000227330 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
CHODL	NM_001204177.2 link	c.-44-165774_-44-165763delAAAAAAAAAAAA	intron_variant	Intron 1 of 4	NP_001191106.1	Q9H9P2A0A0C4DFS2
CHODL	NM_001204178.2 link	c.-45+62764_-45+62775delAAAAAAAAAAAA	intron_variant	Intron 2 of 5	NP_001191107.1	Q9H9P2A0A0C4DFS2
CHODL	NM_001204175.2 link	c.-44-165774_-44-165763delAAAAAAAAAAAA	intron_variant	Intron 1 of 5	NP_001191104.1	Q9H9P2-2
CHODL	NM_001204176.2 link	c.-45+62764_-45+62775delAAAAAAAAAAAA	intron_variant	Intron 2 of 6	NP_001191105.1	Q9H9P2-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
CHODL	ENST00000400131.5 link	c.-44-165782_-44-165771delAAAAAAAAAAAA	intron_variant	Intron 1 of 4	1	ENSP00000382996.1	A0A0C4DFS2
CHODL	ENST00000400135.5 link	c.-45+62756_-45+62767delAAAAAAAAAAAA	intron_variant	Intron 2 of 5	1	ENSP00000383001.1	A0A0C4DFS2
CHODL	ENST00000400127.5 link	c.-45+62756_-45+62767delAAAAAAAAAAAA	intron_variant	Intron 2 of 6	1	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.