chr21-17989995-C-T

Position:

• chr21-17989995-C-T

Variant summary

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

The ENST00000400131.5(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 ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHODL	NM_001204175.2	c.-45+72595C>T		intron_variant
CHODL	NM_001204176.2	c.-144-37877C>T		intron_variant
CHODL	NM_001204177.2	c.-45+72595C>T		intron_variant
CHODL	NM_001204178.2	c.-144-37877C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHODL	ENST00000400127.5	c.-144-37877C>T		intron_variant		1
CHODL	ENST00000400131.5	c.-45+72595C>T		intron_variant		1
CHODL	ENST00000400135.5	c.-144-37877C>T		intron_variant		1
CHODL	ENST00000400128.5	c.-45+72595C>T		intron_variant		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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.654

Alfa AF: 0.723 Hom.: 80444

Bravo AF: 0.636

Asia WGS AF: 0.606 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150210; hg19: chr21-19362312;