rs5842674

chr21-18090726-G-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAchr21-18090726-GAAAAAAAAAAAA-Gchr21-18090726-G-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAACTAAAAAAATTCAAAAAACTTGCTCTTATAATTTCCAchr21-18090726-GAAA-Gchr21-18090726-G-GAAAAAAAAchr21-18090726-G-GAAchr21-18090726-GAAAAAAA-Gchr21-18090726-G-GAAAAAAAchr21-18090726-GAAAAA-Gchr21-18090726-G-GAAAAAchr21-18090726-G-GAAAAchr21-18090726-G-GAAAAAAchr21-18090726-GAAAA-Gchr21-18090726-GAAAAAA-Gchr21-18090726-G-GAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr21-18090726-G-GAchr21-18090726-GA-Gchr21-18090726-G-GAAAchr21-18090726-GAAAAAAAA-Gchr21-18090726-GAA-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000400131.5(CHODL):c.-44-165763_-44-165762insAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000799 in 125,188 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000080 (0 hom., cov: 0)
• Consequence: CHODL ENST00000400131.5 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]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHODL	NM_001204175.2	c.-44-165763_-44-165762insAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAA		intron_variant
CHODL	NM_001204176.2	c.-45+62775_-45+62776insAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAA		intron_variant
CHODL	NM_001204177.2	c.-44-165763_-44-165762insAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAA		intron_variant
CHODL	NM_001204178.2	c.-45+62775_-45+62776insAAAAAAAAAAAAAAAGTAAAATAAAAATTTAAAAATTTAAGAAAATTCATATTATAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432412.1	n.224+9206_224+9207insTTTTTTGAAATTATAATATGAATTTTCTTAAATTTTTAAATTTTTATTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00000799 AC: 1 AN: 125188 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000311

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000799 AC: 1 AN: 125188 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 59456

Gnomad4 AFR AF: 0.0000311

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;