rs1051526

Positions:

• chr21-18267174-G-T

Variant summary

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

The NM_024944.3(CHODL):​c.*1136G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,128 control chromosomes in the GnomAD database, including 3,430 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 0.21 (3430 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: CHODL NM_024944.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHODL	NM_024944.3	c.*1136G>T		3_prime_UTR_variant	6/6	ENST00000299295.7	NP_079220.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000299295.7	c.*1136G>T		3_prime_UTR_variant	6/6	1	NM_024944.3	ENSP00000299295.2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31222 AN: 151998 Hom.: 3417 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.205 AC: 31255 AN: 152116 Hom.: 3430 Cov.: 32 AF XY: 0.203 AC XY: 15100 AN XY: 74370

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.197

Alfa AF: 0.198 Hom.: 1284

Bravo AF: 0.202

Asia WGS AF: 0.117 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.63
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1051526; hg19: chr21-19639491;