chr21-18109036-G-A

Variant names:

• chr21-18109036-G-A
• rs2055011
• ENST00000400131.5:c.-44-147473G>A

Variant summary

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

The ENST00000400131.5(CHODL):​c.-44-147473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,460 control chromosomes in the GnomAD database, including 45,147 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 0.76 (45147 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-44-147473G>A		intron_variant	Intron 1 of 4		NP_001191106.1
CHODL	NM_001204178.2	c.-45+81065G>A		intron_variant	Intron 2 of 5		NP_001191107.1
CHODL	NM_001204175.2	c.-44-147473G>A		intron_variant	Intron 1 of 5		NP_001191104.1
CHODL	NM_001204176.2	c.-45+81065G>A		intron_variant	Intron 2 of 6		NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-44-147473G>A		intron_variant	Intron 1 of 4	1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-45+81065G>A		intron_variant	Intron 2 of 5	1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-45+81065G>A		intron_variant	Intron 2 of 6	1		ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 114998 AN: 151342 Hom.: 45139 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.760 AC: 115042 AN: 151460 Hom.: 45147 Cov.: 32 AF XY: 0.761 AC XY: 56353 AN XY: 74018

African (AFR) AF: 0.542 AC: 22242 AN: 41052

American (AMR) AF: 0.816 AC: 12449 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2966 AN: 3462

East Asian (EAS) AF: 0.860 AC: 4436 AN: 5156

South Asian (SAS) AF: 0.716 AC: 3432 AN: 4796

European-Finnish (FIN) AF: 0.884 AC: 9322 AN: 10550

Middle Eastern (MID) AF: 0.870 AC: 254 AN: 292

European-Non Finnish (NFE) AF: 0.847 AC: 57500 AN: 67892

Other (OTH) AF: 0.796 AC: 1673 AN: 2102

Alfa AF: 0.817 Hom.: 70819

Bravo AF: 0.745

Asia WGS AF: 0.777 AC: 2699 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.9
DANN	Benign	0.61
PhyloP100		0.65
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: rs2055011; hg19: chr21-19481354;