rs2824577

Positions:

• chr21-17959812-A-C
• chr21-17959812-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001204177.2(CHODL):​c.-45+42412A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-45+42412A>C		intron_variant			NP_001191106.1
CHODL	NM_001204178.2	c.-145+42412A>C		intron_variant			NP_001191107.1
CHODL	NM_001204175.2	c.-45+42412A>C		intron_variant			NP_001191104.1
CHODL	NM_001204176.2	c.-145+42412A>C		intron_variant			NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-45+42412A>C		intron_variant		1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-145+42412A>C		intron_variant		1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-145+42412A>C		intron_variant		1		ENSP00000382992.1
CHODL	ENST00000400128.5	c.-45+42412A>C		intron_variant		2		ENSP00000382993.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2824577; hg19: chr21-19332129;