21-17959812-A-G

Variant names:

• chr21-17959812-A-G
• rs2824577
• ENST00000400131.5:c.-45+42412A>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+42412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,028 control chromosomes in the GnomAD database, including 9,085 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 0.34 (9085 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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+42412A>G		intron	N/A	NP_001191106.1
	CHODL	NM_001204178.2		c.-145+42412A>G		intron	N/A	NP_001191107.1
	CHODL	NM_001204175.2		c.-45+42412A>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+42412A>G		intron	N/A	ENSP00000382996.1
	CHODL	ENST00000400135.5	TSL:1	c.-145+42412A>G		intron	N/A	ENSP00000383001.1
	CHODL	ENST00000400127.5	TSL:1	c.-145+42412A>G		intron	N/A	ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51496 AN: 151910 Hom.: 9070 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.339 AC: 51564 AN: 152028 Hom.: 9085 Cov.: 32 AF XY: 0.343 AC XY: 25533 AN XY: 74332

African (AFR) AF: 0.404 AC: 16735 AN: 41448

American (AMR) AF: 0.376 AC: 5746 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5178

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4818

European-Finnish (FIN) AF: 0.280 AC: 2966 AN: 10574

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.287 AC: 19476 AN: 67966

Other (OTH) AF: 0.343 AC: 723 AN: 2108

Alfa AF: 0.303 Hom.: 12682

Bravo AF: 0.342

Asia WGS AF: 0.487 AC: 1688 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.47
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: rs2824577; hg19: chr21-19332129;