Genetic Variant CHODL:c.-44-165783_-44-165782insAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCA (chr21-18090726-G-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001204177.2(CHODL):c.-44-165763_-44-165762insAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAAAAAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000080 ( 0 hom., cov: 0)

Consequence

CHODL
NM_001204177.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found

Variant links:

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]

CHODL links:

ENSG00000227330 (HGNC:58357):

ENSG00000227330 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
CHODL	NM_001204177.2	c.-44-165763_-44-165762insAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAAAAAAAAAAAAAAAAAAAAA	intron	N/A	NP_001191106.1	A0A0C4DFS2
CHODL	NM_001204178.2	c.-45+62775_-45+62776insAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAAAAAAAAAAAAAAAAAAAAA	intron	N/A	NP_001191107.1	A0A0C4DFS2
CHODL	NM_001204175.2	c.-44-165763_-44-165762insAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAAAAAAAAAAAAAAAAAAAAA	intron	N/A	NP_001191104.1	Q9H9P2-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHODL	ENST00000400131.5	TSL:1	c.-44-165783_-44-165782insAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCA	intron	N/A	ENSP00000382996.1	A0A0C4DFS2
CHODL	ENST00000400135.5	TSL:1	c.-45+62755_-45+62756insAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCA	intron	N/A	ENSP00000383001.1	A0A0C4DFS2
CHODL	ENST00000400127.5	TSL:1	c.-45+62755_-45+62756insAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCA	intron	N/A	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes

AF:

0.00000799

AC:

AN:

125188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000160

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00000799

AC:

AN:

125188

Hom.:

Cov.:

AF XY:

0.0000168

AC XY:

AN XY:

59456

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

32194

American (AMR)

AF:

0.00

AC:

AN:

12182

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3206

East Asian (EAS)

AF:

0.00

AC:

AN:

2688

South Asian (SAS)

AF:

0.00

AC:

AN:

3602

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6018

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000160

AC:

AN:

62492

Other (OTH)

AF:

0.00

AC:

AN:

1730

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

21-18090726-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAAAAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over