chr21-18090726-GA-G

Variant names:

• chr21-18090726-GA-G
• rs5842674
• ENST00000400131.5:c.-44-165782delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000400131.5(CHODL):​c.-44-165782delA 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 0.10 (552 hom., cov: 0)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

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]

ENSG00000227330 (HGNC:58357):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400131.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	NM_001204177.2		c.-44-165763delA		intron	N/A	NP_001191106.1
	CHODL	NM_001204178.2		c.-45+62775delA		intron	N/A	NP_001191107.1
	CHODL	NM_001204175.2		c.-44-165763delA		intron	N/A	NP_001191104.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	ENST00000400131.5	TSL:1	c.-44-165782delA		intron	N/A	ENSP00000382996.1
	CHODL	ENST00000400135.5	TSL:1	c.-45+62756delA		intron	N/A	ENSP00000383001.1
	CHODL	ENST00000400127.5	TSL:1	c.-45+62756delA		intron	N/A	ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 12839 AN: 124628 Hom.: 552 Cov.: 0

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.103 AC: 12830 AN: 124616 Hom.: 552 Cov.: 0 AF XY: 0.105 AC XY: 6197 AN XY: 59180

African (AFR) AF: 0.0380 AC: 1222 AN: 32156

American (AMR) AF: 0.125 AC: 1512 AN: 12134

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 376 AN: 3196

East Asian (EAS) AF: 0.236 AC: 634 AN: 2684

South Asian (SAS) AF: 0.210 AC: 748 AN: 3554

European-Finnish (FIN) AF: 0.133 AC: 794 AN: 5980

Middle Eastern (MID) AF: 0.127 AC: 27 AN: 212

European-Non Finnish (NFE) AF: 0.116 AC: 7238 AN: 62142

Other (OTH) AF: 0.117 AC: 202 AN: 1726

Alfa AF: 0.0816 Hom.: 412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463044; COSMIC: COSV68043639;