21-18090726-GAA-G

Position:

• chr21-18090726-GAA-G

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
• 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]

(HGNC:):

ACMG classification

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: 164 AN: 125180 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000248

Gnomad AMI AF: 0.00477

Gnomad AMR AF: 0.00115

Gnomad ASJ AF: 0.00250

Gnomad EAS AF: 0.00298

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.000499

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00125

Gnomad OTH AF: 0.00173

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

GnomAD4 genome AF: 0.00131 AC: 164 AN: 125164 Hom.: 2 Cov.: 0 AF XY: 0.00172 AC XY: 102 AN XY: 59460

Gnomad4 AFR AF: 0.000248

Gnomad4 AMR AF: 0.00115

Gnomad4 ASJ AF: 0.00250

Gnomad4 EAS AF: 0.00298

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.000499

Gnomad4 NFE AF: 0.00125

Gnomad4 OTH AF: 0.00173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463044;