21-18052888-T-G

Variant names:

• chr21-18052888-T-G
• rs494619
• ENST00000400131.5:c.-45+135488T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400131.5(CHODL):​c.-45+135488T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,748 control chromosomes in the GnomAD database, including 5,034 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (5034 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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.-45+135488T>G		intron	N/A	NP_001191106.1
	CHODL	NM_001204178.2		c.-45+24917T>G		intron	N/A	NP_001191107.1
	CHODL	NM_001204175.2		c.-45+135488T>G		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.-45+135488T>G		intron	N/A	ENSP00000382996.1
	CHODL	ENST00000400135.5	TSL:1	c.-45+24917T>G		intron	N/A	ENSP00000383001.1
	CHODL	ENST00000400127.5	TSL:1	c.-45+24917T>G		intron	N/A	ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24821 AN: 151630 Hom.: 5014 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0194

Gnomad EAS AF: 0.00484

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.164 AC: 24879 AN: 151748 Hom.: 5034 Cov.: 32 AF XY: 0.162 AC XY: 12010 AN XY: 74204

African (AFR) AF: 0.479 AC: 19771 AN: 41262

American (AMR) AF: 0.0739 AC: 1126 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0194 AC: 67 AN: 3462

East Asian (EAS) AF: 0.00485 AC: 25 AN: 5158

South Asian (SAS) AF: 0.104 AC: 500 AN: 4816

European-Finnish (FIN) AF: 0.0318 AC: 338 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0397 AC: 2692 AN: 67886

Other (OTH) AF: 0.124 AC: 260 AN: 2102

Alfa AF: 0.251 Hom.: 1925

Bravo AF: 0.180

Asia WGS AF: 0.0750 AC: 263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.46
PhyloP100		-0.18
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: rs494619; hg19: chr21-19425206;