rs200801

chr21-17961329-G-Achr21-17961329-G-C

Variant summary

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

The ENST00000400131.5(CHODL):c.-45+43929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,040 control chromosomes in the GnomAD database, including 16,539 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 0.46 (16539 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHODL	NM_001204175.2	c.-45+43929G>A		intron_variant
CHODL	NM_001204176.2	c.-145+43929G>A		intron_variant
CHODL	NM_001204177.2	c.-45+43929G>A		intron_variant
CHODL	NM_001204178.2	c.-145+43929G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHODL	ENST00000400127.5	c.-145+43929G>A		intron_variant		1
CHODL	ENST00000400131.5	c.-45+43929G>A		intron_variant		1
CHODL	ENST00000400135.5	c.-145+43929G>A		intron_variant		1
CHODL	ENST00000400128.5	c.-45+43929G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69454 AN: 151922 Hom.: 16523 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.457 AC: 69520 AN: 152040 Hom.: 16539 Cov.: 32 AF XY: 0.453 AC XY: 33626 AN XY: 74290

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.476

Alfa AF: 0.449 Hom.: 20402

Bravo AF: 0.471

Asia WGS AF: 0.279 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.010
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200801; hg19: chr21-19333646;