21-17989995-C-T

Variant names:

• chr21-17989995-C-T
• rs150210
• ENST00000400131.5:c.-45+72595C>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+72595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,780 control chromosomes in the GnomAD database, including 32,909 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 0.64 (32909 hom., cov: 31)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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+72595C>T		intron	N/A	NP_001191106.1	A0A0C4DFS2
	CHODL	NM_001204178.2		c.-144-37877C>T		intron	N/A	NP_001191107.1	A0A0C4DFS2
	CHODL	NM_001204175.2		c.-45+72595C>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+72595C>T		intron	N/A	ENSP00000382996.1	A0A0C4DFS2
	CHODL	ENST00000400135.5	TSL:1	c.-144-37877C>T		intron	N/A	ENSP00000383001.1	A0A0C4DFS2
	CHODL	ENST00000400127.5	TSL:1	c.-144-37877C>T		intron	N/A	ENSP00000382992.1	Q9H9P2-2

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97786 AN: 151662 Hom.: 32913 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.644 AC: 97815 AN: 151780 Hom.: 32909 Cov.: 31 AF XY: 0.642 AC XY: 47599 AN XY: 74176

African (AFR) AF: 0.434 AC: 17960 AN: 41358

American (AMR) AF: 0.692 AC: 10547 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2142 AN: 3468

East Asian (EAS) AF: 0.740 AC: 3809 AN: 5148

South Asian (SAS) AF: 0.569 AC: 2733 AN: 4804

European-Finnish (FIN) AF: 0.720 AC: 7599 AN: 10552

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50738 AN: 67904

Other (OTH) AF: 0.654 AC: 1376 AN: 2104

Alfa AF: 0.706 Hom.: 126251

Bravo AF: 0.636

Asia WGS AF: 0.606 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.9
DANN	Benign	0.81
PhyloP100		0.22
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: rs150210; hg19: chr21-19362312;