chr21-18090726-GAAAAAAA-G

Variant names:

• chr21-18090725-AGAAAAAA-AG
• rs5842674
• ENST00000400131.5:c.-44-165782_-44-165777delAAAAAA

Variant summary

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

The NM_001204177.2(CHODL):​c.-44-165768_-44-165763delAAAAAA 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 0.43 (11473 hom., cov: 0)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• 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 (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204177.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	NM_001204177.2		c.-44-165768_-44-165763delAAAAAA		intron	N/A	NP_001191106.1	A0A0C4DFS2
	CHODL	NM_001204178.2		c.-45+62770_-45+62775delAAAAAA		intron	N/A	NP_001191107.1	A0A0C4DFS2
	CHODL	NM_001204175.2		c.-44-165768_-44-165763delAAAAAA		intron	N/A	NP_001191104.1	Q9H9P2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	ENST00000400131.5	TSL:1	c.-44-165782_-44-165777delAAAAAA		intron	N/A	ENSP00000382996.1	A0A0C4DFS2
	CHODL	ENST00000400135.5	TSL:1	c.-45+62756_-45+62761delAAAAAA		intron	N/A	ENSP00000383001.1	A0A0C4DFS2
	CHODL	ENST00000400127.5	TSL:1	c.-45+62756_-45+62761delAAAAAA		intron	N/A	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 54454 AN: 125400 Hom.: 11475 Cov.: 0

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.0784

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.434 AC: 54447 AN: 125384 Hom.: 11473 Cov.: 0 AF XY: 0.432 AC XY: 25769 AN XY: 59584

African (AFR) AF: 0.292 AC: 9409 AN: 32272

American (AMR) AF: 0.426 AC: 5194 AN: 12194

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1497 AN: 3204

East Asian (EAS) AF: 0.0786 AC: 211 AN: 2686

South Asian (SAS) AF: 0.284 AC: 1015 AN: 3570

European-Finnish (FIN) AF: 0.517 AC: 3127 AN: 6052

Middle Eastern (MID) AF: 0.495 AC: 110 AN: 222

European-Non Finnish (NFE) AF: 0.521 AC: 32612 AN: 62602

Other (OTH) AF: 0.455 AC: 792 AN: 1740

Alfa AF: 0.406 Hom.: 412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463043;