21-18090726-GAAAA-G

Variant names:

• chr21-18090725-AGAAA-AG
• rs5842674
• ENST00000400131.5:c.-44-165782_-44-165780delAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001204177.2(CHODL):​c.-44-165765_-44-165763delAAA 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 0.000032 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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.-44-165765_-44-165763delAAA		intron	N/A	NP_001191106.1	A0A0C4DFS2
	CHODL	NM_001204178.2		c.-45+62773_-45+62775delAAA		intron	N/A	NP_001191107.1	A0A0C4DFS2
	CHODL	NM_001204175.2		c.-44-165765_-44-165763delAAA		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_-44-165780delAAA		intron	N/A	ENSP00000382996.1	A0A0C4DFS2
	CHODL	ENST00000400135.5	TSL:1	c.-45+62756_-45+62758delAAA		intron	N/A	ENSP00000383001.1	A0A0C4DFS2
	CHODL	ENST00000400127.5	TSL:1	c.-45+62756_-45+62758delAAA		intron	N/A	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes AF: 0.0000320 AC: 4 AN: 125188 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000311

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000372

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000160

Gnomad OTH AF: 0.000578

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

GnomAD4 genome AF: 0.0000320 AC: 4 AN: 125172 Hom.: 0 Cov.: 0 AF XY: 0.0000336 AC XY: 2 AN XY: 59464

African (AFR) AF: 0.0000310 AC: 1 AN: 32238

American (AMR) AF: 0.00 AC: 0 AN: 12180

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3206

East Asian (EAS) AF: 0.000373 AC: 1 AN: 2684

South Asian (SAS) AF: 0.00 AC: 0 AN: 3574

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.0000160 AC: 1 AN: 62482

Other (OTH) AF: 0.000577 AC: 1 AN: 1734

Alfa AF: 0.00 Hom.: 412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.85

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;