21-18090726-GAAAAAAAAAAAA-GAAAAAAAAAAAAA

Variant names:

• chr21-18090726-G-GA
• rs5842674
• ENST00000400131.5:c.-44-165783_-44-165782insA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000400131.5(CHODL):​c.-44-165783_-44-165782insA 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 0.17 (2040 hom., cov: 0)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-44-165763dupA		intron_variant	Intron 1 of 4		NP_001191106.1
CHODL	NM_001204178.2	c.-45+62775dupA		intron_variant	Intron 2 of 5		NP_001191107.1
CHODL	NM_001204175.2	c.-44-165763dupA		intron_variant	Intron 1 of 5		NP_001191104.1
CHODL	NM_001204176.2	c.-45+62775dupA		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.-44-165783_-44-165782insA		intron_variant	Intron 1 of 4	1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-45+62755_-45+62756insA		intron_variant	Intron 2 of 5	1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-45+62755_-45+62756insA		intron_variant	Intron 2 of 6	1		ENSP00000382992.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 21580 AN: 124390 Hom.: 2037 Cov.: 0

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.174 AC: 21582 AN: 124370 Hom.: 2040 Cov.: 0 AF XY: 0.168 AC XY: 9922 AN XY: 59044

African (AFR) AF: 0.228 AC: 7306 AN: 32012

American (AMR) AF: 0.145 AC: 1753 AN: 12084

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 565 AN: 3190

East Asian (EAS) AF: 0.0239 AC: 64 AN: 2678

South Asian (SAS) AF: 0.157 AC: 556 AN: 3552

European-Finnish (FIN) AF: 0.116 AC: 682 AN: 5882

Middle Eastern (MID) AF: 0.121 AC: 26 AN: 214

European-Non Finnish (NFE) AF: 0.164 AC: 10209 AN: 62188

Other (OTH) AF: 0.162 AC: 280 AN: 1730

Alfa AF: 0.0980 Hom.: 412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.0
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: rs5842674; hg19: chr21-19463044;