21-18090726-GAAAAAAAAAAAA-GAAAAAAAAAAA

Variant names:

• chr21-18090726-GA-G
• rs5842674
• ENST00000400131.5:c.-44-165782delA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001204177.2(CHODL):​c.-44-165763delA 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 0.10 (552 hom., cov: 0)
• Consequence: CHODL NM_001204177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 12839 AN: 124628 Hom.: 552 Cov.: 0

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.103 AC: 12830 AN: 124616 Hom.: 552 Cov.: 0 AF XY: 0.105 AC XY: 6197 AN XY: 59180

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5842674; hg19: chr21-19463044;