NM_024944.3:c.80-3601C>A

Variant names:

• chr21-18252908-C-A
• rs7279148
• NM_024944.3:c.80-3601C>A

Variant summary

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

The NM_024944.3(CHODL):​c.80-3601C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,936 control chromosomes in the GnomAD database, including 6,842 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 0.27 (6842 hom., cov: 31)
• Consequence: CHODL NM_024944.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_024944.3	c.80-3601C>A		intron_variant	Intron 1 of 5	ENST00000299295.7	NP_079220.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000299295.7	c.80-3601C>A		intron_variant	Intron 1 of 5	1	NM_024944.3	ENSP00000299295.2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40879 AN: 151818 Hom.: 6840 Cov.: 31

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.269 AC: 40887 AN: 151936 Hom.: 6842 Cov.: 31 AF XY: 0.271 AC XY: 20140 AN XY: 74220

African (AFR) AF: 0.0729 AC: 3025 AN: 41470

American (AMR) AF: 0.310 AC: 4726 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3468

East Asian (EAS) AF: 0.171 AC: 880 AN: 5160

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4804

European-Finnish (FIN) AF: 0.448 AC: 4718 AN: 10524

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23972 AN: 67934

Other (OTH) AF: 0.280 AC: 589 AN: 2106

Alfa AF: 0.308 Hom.: 10434

Bravo AF: 0.253

Asia WGS AF: 0.224 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.81
PhyloP100		0.047
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7279148; hg19: chr21-19625225;