dbSNP rs1189009907: CHODL:p.Ala188Asp (chr21-18260215-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024944.3(CHODL):c.563C>A(p.Ala188Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A188V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CHODL
NM_024944.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.315

Publications

0 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]

CHODL links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.033111095).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024944.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CHODL	NM_024944.3	MANE Select	c.563C>A	p.Ala188Asp	missense	Exon 4 of 6	NP_079220.2
CHODL	NM_001204174.2		c.506C>A	p.Ala169Asp	missense	Exon 4 of 6	NP_001191103.1	Q9H9P2-4
CHODL	NM_001204177.2		c.440C>A	p.Ala147Asp	missense	Exon 4 of 5	NP_001191106.1	A0A0C4DFS2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CHODL	ENST00000299295.7	TSL:1 MANE Select	c.563C>A	p.Ala188Asp	missense	Exon 4 of 6	ENSP00000299295.2	Q9H9P2-1
CHODL	ENST00000400131.5	TSL:1	c.440C>A	p.Ala147Asp	missense	Exon 4 of 5	ENSP00000382996.1	A0A0C4DFS2
CHODL	ENST00000400135.5	TSL:1	c.440C>A	p.Ala147Asp	missense	Exon 5 of 6	ENSP00000383001.1	A0A0C4DFS2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1418294

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

705032

African (AFR)

AF:

0.00

AC:

AN:

31146

American (AMR)

AF:

0.00

AC:

AN:

38092

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25260

East Asian (EAS)

AF:

0.00

AC:

AN:

36982

South Asian (SAS)

AF:

0.00

AC:

AN:

78462

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52820

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5646

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1091286

Other (OTH)

AF:

0.00

AC:

AN:

58600

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.1

(source)

DANN

Benign

0.64

DEOGEN2

Benign

0.030

Eigen

Benign

-0.95

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.52

M_CAP

Benign

0.0065

MetaRNN

Benign

0.033

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.55

PhyloP100

0.32

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.1

REVEL

Benign

0.024

Sift

Benign

0.46

Sift4G

Benign

0.44

Polyphen

0.0

Vest4

0.080

MutPred

0.30

Gain of disorder (P = 0.039)

MVP

0.099

MPC

0.091

ClinPred

0.041

GERP RS

1.8

Varity_R

0.089

gMVP

0.51

Mutation Taster

=93/7

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over