rs6517799
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000400131.5(CHODL):c.-44-103608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0375 in 152,304 control chromosomes in the GnomAD database, including 343 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 0.037 ( 343 hom., cov: 32)
Consequence
CHODL
ENST00000400131.5 intron
ENST00000400131.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0610
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHODL | NM_001204175.2 | c.-44-103608A>G | intron_variant | ||||
CHODL | NM_001204176.2 | c.-44-103608A>G | intron_variant | ||||
CHODL | NM_001204177.2 | c.-44-103608A>G | intron_variant | ||||
CHODL | NM_001204178.2 | c.-44-103608A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHODL | ENST00000400127.5 | c.-44-103608A>G | intron_variant | 1 | |||||
CHODL | ENST00000400131.5 | c.-44-103608A>G | intron_variant | 1 | |||||
CHODL | ENST00000400135.5 | c.-44-103608A>G | intron_variant | 1 | |||||
CHODL | ENST00000400128.5 | c.-44-103608A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0373 AC: 5682AN: 152186Hom.: 337 Cov.: 32
GnomAD3 genomes
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152186
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0375 AC: 5711AN: 152304Hom.: 343 Cov.: 32 AF XY: 0.0361 AC XY: 2692AN XY: 74484
GnomAD4 genome
?
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AC:
5711
AN:
152304
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32
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2692
AN XY:
74484
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41
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at