ENST00000400131.5:c.-45+45914C>T

Variant names:

• chr21-17963314-C-T
• rs2254434
• ENST00000400131.5:c.-45+45914C>T

Variant summary

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

The ENST00000400131.5(CHODL):​c.-45+45914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,958 control chromosomes in the GnomAD database, including 9,821 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 0.35 (9821 hom., cov: 32)
• Consequence: CHODL ENST00000400131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHODL	NM_001204177.2	c.-45+45914C>T		intron_variant	Intron 1 of 4		NP_001191106.1
CHODL	NM_001204178.2	c.-145+45914C>T		intron_variant	Intron 1 of 5		NP_001191107.1
CHODL	NM_001204175.2	c.-45+45914C>T		intron_variant	Intron 1 of 5		NP_001191104.1
CHODL	NM_001204176.2	c.-145+45914C>T		intron_variant	Intron 1 of 6		NP_001191105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHODL	ENST00000400131.5	c.-45+45914C>T		intron_variant	Intron 1 of 4	1		ENSP00000382996.1
CHODL	ENST00000400135.5	c.-145+45914C>T		intron_variant	Intron 1 of 5	1		ENSP00000383001.1
CHODL	ENST00000400127.5	c.-145+45914C>T		intron_variant	Intron 1 of 6	1		ENSP00000382992.1
CHODL	ENST00000400128.5	c.-45+45914C>T		intron_variant	Intron 2 of 6	2		ENSP00000382993.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53050 AN: 151840 Hom.: 9818 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.349 AC: 53071 AN: 151958 Hom.: 9821 Cov.: 32 AF XY: 0.350 AC XY: 25990 AN XY: 74236

African (AFR) AF: 0.283 AC: 11736 AN: 41450

American (AMR) AF: 0.368 AC: 5626 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3464

East Asian (EAS) AF: 0.661 AC: 3414 AN: 5168

South Asian (SAS) AF: 0.204 AC: 984 AN: 4820

European-Finnish (FIN) AF: 0.430 AC: 4520 AN: 10518

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24850 AN: 67954

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.349 Hom.: 29880

Bravo AF: 0.346

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.64
PhyloP100		0.37
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: rs2254434; hg19: chr21-19335631;