rs982274

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000400131.5(CHODL):​c.-44-149096G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,066 control chromosomes in the GnomAD database, including 11,455 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 0.36 ( 11455 hom., cov: 32)

Consequence

CHODL
ENST00000400131.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.922

Publications

5 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHODLNM_001204177.2 linkc.-44-149096G>T intron_variant Intron 1 of 4 NP_001191106.1 Q9H9P2A0A0C4DFS2
CHODLNM_001204178.2 linkc.-45+79442G>T intron_variant Intron 2 of 5 NP_001191107.1 Q9H9P2A0A0C4DFS2
CHODLNM_001204175.2 linkc.-44-149096G>T intron_variant Intron 1 of 5 NP_001191104.1 Q9H9P2-2
CHODLNM_001204176.2 linkc.-45+79442G>T intron_variant Intron 2 of 6 NP_001191105.1 Q9H9P2-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHODLENST00000400131.5 linkc.-44-149096G>T intron_variant Intron 1 of 4 1 ENSP00000382996.1 A0A0C4DFS2
CHODLENST00000400135.5 linkc.-45+79442G>T intron_variant Intron 2 of 5 1 ENSP00000383001.1 A0A0C4DFS2
CHODLENST00000400127.5 linkc.-45+79442G>T intron_variant Intron 2 of 6 1 ENSP00000382992.1 Q9H9P2-2

Frequencies

GnomAD3 genomes
AF:
0.357
AC:
54268
AN:
151948
Hom.:
11459
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.476
Gnomad AMR
AF:
0.367
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.0275
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.394
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.496
Gnomad OTH
AF:
0.404
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.357
AC:
54260
AN:
152066
Hom.:
11455
Cov.:
32
AF XY:
0.350
AC XY:
25975
AN XY:
74318
show subpopulations
African (AFR)
AF:
0.161
AC:
6692
AN:
41520
American (AMR)
AF:
0.367
AC:
5600
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.424
AC:
1470
AN:
3470
East Asian (EAS)
AF:
0.0272
AC:
141
AN:
5180
South Asian (SAS)
AF:
0.234
AC:
1130
AN:
4822
European-Finnish (FIN)
AF:
0.394
AC:
4154
AN:
10550
Middle Eastern (MID)
AF:
0.415
AC:
122
AN:
294
European-Non Finnish (NFE)
AF:
0.496
AC:
33678
AN:
67940
Other (OTH)
AF:
0.398
AC:
840
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1628
3255
4883
6510
8138
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
510
1020
1530
2040
2550
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.450
Hom.:
41343
Bravo
AF:
0.344
Asia WGS
AF:
0.139
AC:
486
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.30
DANN
Benign
0.24
PhyloP100
-0.92
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs982274; hg19: chr21-19479731; API