Genetic Variant CLEC11A:p.Glu195Lys (chr19-50725078-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002975.3(CLEC11A):c.583G>A(p.Glu195Lys) 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CLEC11A
NM_002975.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.37

Publications

0 publications found

Variant links:

Genes affected

CLEC11A (HGNC:10576): (C-type lectin domain containing 11A) This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]

CLEC11A links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16222844).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002975.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC11A	NM_002975.3	MANE Select	c.583G>A	p.Glu195Lys	missense	Exon 4 of 4	NP_002966.1	Q9Y240

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CLEC11A	ENST00000250340.9	TSL:1 MANE Select	c.583G>A	p.Glu195Lys	missense	Exon 4 of 4	ENSP00000250340.3	Q9Y240
CLEC11A	ENST00000599973.1	TSL:1	c.632G>A	p.Arg211Gln	missense	Exon 4 of 4	ENSP00000471075.1	M0R081
CLEC11A	ENST00000883282.1		c.574G>A	p.Glu192Lys	missense	Exon 4 of 4	ENSP00000553341.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1369478

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

674650

African (AFR)

AF:

0.00

AC:

AN:

29316

American (AMR)

AF:

0.00

AC:

AN:

30630

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23356

East Asian (EAS)

AF:

0.00

AC:

AN:

34610

South Asian (SAS)

AF:

0.00

AC:

AN:

75292

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45130

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5570

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1068796

Other (OTH)

AF:

0.00

AC:

AN:

56778

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.63

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.55

CADD

Pathogenic

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.052

Eigen

Benign

-0.23

Eigen_PC

Benign

-0.25

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.84

M_CAP

Uncertain

0.11

MetaRNN

Benign

0.16

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.11

PhyloP100

3.4

PrimateAI

Pathogenic

0.92

PROVEAN

Benign

0.93

REVEL

Benign

0.18

Sift

Benign

0.90

Sift4G

Uncertain

0.013

Polyphen

0.99

Vest4

0.16

MutPred

0.56

Gain of MoRF binding (P = 0.0013)

MVP

0.55

MPC

0.90

ClinPred

0.91

GERP RS

1.8

Varity_R

0.12

gMVP

0.66

Mutation Taster

=51/49

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