21-18159125-A-C

Position:

• chr21-18159125-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000400131.5(CHODL):​c.-44-97384A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,282 control chromosomes in the GnomAD database, including 85 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 0.025 (85 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.79).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0252 (3831/152282) while in subpopulation NFE AF= 0.0419 (2852/68018). AF 95% confidence interval is 0.0406. There are 85 homozygotes in gnomad4. There are 1767 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 85 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHODL	NM_001204175.2	c.-44-97384A>C		intron_variant			NP_001191104.1
CHODL	NM_001204176.2	c.-44-97384A>C		intron_variant			NP_001191105.1
CHODL	NM_001204177.2	c.-44-97384A>C		intron_variant			NP_001191106.1
CHODL	NM_001204178.2	c.-44-97384A>C		intron_variant			NP_001191107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400127.5	c.-44-97384A>C		intron_variant		1		ENSP00000382992
CHODL	ENST00000400131.5	c.-44-97384A>C		intron_variant		1		ENSP00000382996
CHODL	ENST00000400135.5	c.-44-97384A>C		intron_variant		1		ENSP00000383001
CHODL	ENST00000400128.5	c.-44-97384A>C		intron_variant		2		ENSP00000382993

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3833 AN: 152164 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00736

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0205

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0252 AC: 3831 AN: 152282 Hom.: 85 Cov.: 32 AF XY: 0.0237 AC XY: 1767 AN XY: 74460

Gnomad4 AFR AF: 0.00734

Gnomad4 AMR AF: 0.0205

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.0108

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0217

Alfa AF: 0.0346 Hom.: 17

Bravo AF: 0.0255

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77600076; hg19: chr21-19531442;