rs494619

Positions:

• chr21-18052888-T-G
• chr21-18052888-T-A
• chr21-18052888-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHODL	NM_001204175.2	c.-45+135488T>G		intron_variant
CHODL	NM_001204176.2	c.-45+24917T>G		intron_variant
CHODL	NM_001204177.2	c.-45+135488T>G		intron_variant
CHODL	NM_001204178.2	c.-45+24917T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432412.1	n.225-18259A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.0739

Gnomad4 ASJ AF: 0.0194

Gnomad4 EAS AF: 0.00485

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.124

Alfa AF: 0.120 Hom.: 433

Bravo AF: 0.180

Asia WGS AF: 0.0750 AC: 263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs494619; hg19: chr21-19425206;