rs158081

Variant names:

• chr21-17996684-G-A
• rs158081
• ENST00000400131.5:c.-45+79284G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400131.5(CHODL):​c.-45+79284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,112 control chromosomes in the GnomAD database, including 38,391 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 0.70 (38391 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-45+79284G>A		intron_variant	Intron 1 of 4		NP_001191106.1
CHODL	NM_001204178.2	c.-144-31188G>A		intron_variant	Intron 1 of 5		NP_001191107.1
CHODL	NM_001204175.2	c.-45+79284G>A		intron_variant	Intron 1 of 5		NP_001191104.1
CHODL	NM_001204176.2	c.-144-31188G>A		intron_variant	Intron 1 of 6		NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-45+79284G>A		intron_variant	Intron 1 of 4	1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-144-31188G>A		intron_variant	Intron 1 of 5	1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-144-31188G>A		intron_variant	Intron 1 of 6	1		ENSP00000382992.1
CHODL	ENST00000400128.5	c.-45+79284G>A		intron_variant	Intron 2 of 6	2		ENSP00000382993.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106248 AN: 151994 Hom.: 38325 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.699 AC: 106373 AN: 152112 Hom.: 38391 Cov.: 32 AF XY: 0.696 AC XY: 51764 AN XY: 74340

African (AFR) AF: 0.867 AC: 36014 AN: 41530

American (AMR) AF: 0.658 AC: 10068 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2606 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1889 AN: 5162

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4818

European-Finnish (FIN) AF: 0.573 AC: 6043 AN: 10550

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43579 AN: 67960

Other (OTH) AF: 0.708 AC: 1496 AN: 2114

Alfa AF: 0.669 Hom.: 57341

Bravo AF: 0.708

Asia WGS AF: 0.636 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		0.033
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: rs158081; hg19: chr21-19369001;