21-17944729-C-T

Variant names:

• chr21-17944729-C-T
• rs9305833
• ENST00000400131.5:c.-45+27329C>T

Variant summary

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

The NM_001204177.2(CHODL):​c.-45+27329C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,214 control chromosomes in the GnomAD database, including 1,876 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 0.15 (1876 hom., cov: 33)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204177.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	NM_001204177.2		c.-45+27329C>T		intron	N/A	NP_001191106.1	A0A0C4DFS2
	CHODL	NM_001204178.2		c.-145+27329C>T		intron	N/A	NP_001191107.1	A0A0C4DFS2
	CHODL	NM_001204175.2		c.-45+27329C>T		intron	N/A	NP_001191104.1	Q9H9P2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHODL	ENST00000400131.5	TSL:1	c.-45+27329C>T		intron	N/A	ENSP00000382996.1	A0A0C4DFS2
	CHODL	ENST00000400135.5	TSL:1	c.-145+27329C>T		intron	N/A	ENSP00000383001.1	A0A0C4DFS2
	CHODL	ENST00000400127.5	TSL:1	c.-145+27329C>T		intron	N/A	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22851 AN: 152096 Hom.: 1880 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.150 AC: 22851 AN: 152214 Hom.: 1876 Cov.: 33 AF XY: 0.145 AC XY: 10788 AN XY: 74424

African (AFR) AF: 0.115 AC: 4779 AN: 41520

American (AMR) AF: 0.153 AC: 2343 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.142 AC: 687 AN: 4828

European-Finnish (FIN) AF: 0.0988 AC: 1048 AN: 10606

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12545 AN: 68012

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.174 Hom.: 4075

Bravo AF: 0.153

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		-0.77
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: rs9305833; hg19: chr21-19317046;