chr21-18090726-GAAAAAAA-G

Variant names:

• chr21-18090726-GAAAAAAA-G
• rs5842674
• ENST00000400131.5:c.-44-165782_-44-165776delAAAAAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000400131.5(CHODL):​c.-44-165782_-44-165776delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0079 (8 hom., cov: 0)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• Publications: 0 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]

ENSG00000227330 (HGNC:58357):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00792 (992/125176) while in subpopulation AFR AF = 0.0221 (711/32242). AF 95% confidence interval is 0.0207. There are 8 homozygotes in GnomAd4. There are 508 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-44-165769_-44-165763delAAAAAAA		intron_variant	Intron 1 of 4		NP_001191106.1
CHODL	NM_001204178.2	c.-45+62769_-45+62775delAAAAAAA		intron_variant	Intron 2 of 5		NP_001191107.1
CHODL	NM_001204175.2	c.-44-165769_-44-165763delAAAAAAA		intron_variant	Intron 1 of 5		NP_001191104.1
CHODL	NM_001204176.2	c.-45+62769_-45+62775delAAAAAAA		intron_variant	Intron 2 of 6		NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-44-165782_-44-165776delAAAAAAA		intron_variant	Intron 1 of 4	1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-45+62756_-45+62762delAAAAAAA		intron_variant	Intron 2 of 5	1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-45+62756_-45+62762delAAAAAAA		intron_variant	Intron 2 of 6	1		ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.00792 AC: 991 AN: 125192 Hom.: 8 Cov.: 0

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00566

Gnomad ASJ AF: 0.00343

Gnomad EAS AF: 0.000372

Gnomad SAS AF: 0.00305

Gnomad FIN AF: 0.00332

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00251

Gnomad OTH AF: 0.00751

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

GnomAD4 genome AF: 0.00792 AC: 992 AN: 125176 Hom.: 8 Cov.: 0 AF XY: 0.00854 AC XY: 508 AN XY: 59470

African (AFR) AF: 0.0221 AC: 711 AN: 32242

American (AMR) AF: 0.00566 AC: 69 AN: 12182

Ashkenazi Jewish (ASJ) AF: 0.00343 AC: 11 AN: 3206

East Asian (EAS) AF: 0.000373 AC: 1 AN: 2684

South Asian (SAS) AF: 0.00280 AC: 10 AN: 3574

European-Finnish (FIN) AF: 0.00332 AC: 20 AN: 6016

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.00251 AC: 157 AN: 62482

Other (OTH) AF: 0.00750 AC: 13 AN: 1734

Alfa AF: 0.00473 Hom.: 412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463044;