rs2824643

Positions:

• chr21-18132538-C-T
• chr21-18132538-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204177.2(CHODL):​c.-44-123971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,026 control chromosomes in the GnomAD database, including 3,074 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 0.17 (3074 hom., cov: 32)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-44-123971C>T		intron_variant			NP_001191106.1
CHODL	NM_001204178.2	c.-45+104567C>T		intron_variant			NP_001191107.1
CHODL	NM_001204175.2	c.-44-123971C>T		intron_variant			NP_001191104.1
CHODL	NM_001204176.2	c.-45+104567C>T		intron_variant			NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-44-123971C>T		intron_variant		1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-45+104567C>T		intron_variant		1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-45+104567C>T		intron_variant		1		ENSP00000382992.1
CHODL	ENST00000400128.5	c.-44-123971C>T		intron_variant		2		ENSP00000382993.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25918 AN: 151910 Hom.: 3069 Cov.: 32

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.171 AC: 25929 AN: 152026 Hom.: 3074 Cov.: 32 AF XY: 0.180 AC XY: 13354 AN XY: 74306

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.160

Alfa AF: 0.176 Hom.: 579

Bravo AF: 0.167

Asia WGS AF: 0.393 AC: 1368 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2824643; hg19: chr21-19504855;