Variant rs16914640 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000290855.11(CLEC2D):c.57C>G(p.Asn19Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,609,426 control chromosomes in the GnomAD database, including 23,083 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 5602 hom., cov: 32)

Exomes 𝑓: 0.14 ( 17481 hom. )

Consequence

CLEC2D
ENST00000290855.11 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Variant links:

Genes affected

CLEC2D (HGNC:14351): (C-type lectin domain family 2 member D) This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]

CLEC2D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.1648746E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC2D	NM_013269.6 linkuse as main transcript	c.57C>G	p.Asn19Lys	missense_variant	1/5	ENST00000290855.11	NP_037401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC2D	ENST00000290855.11 linkuse as main transcript	c.57C>G	p.Asn19Lys	missense_variant	1/5	1	NM_013269.6	ENSP00000290855	P2	Q9UHP7-1

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34496

AN:

151742

Hom.:

5590

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.0527

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.0129

Gnomad SAS

AF:

0.0772

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.196

GnomAD3 exomes

AF:

0.143

AC:

35775

AN:

251042

Hom.:

3719

AF XY:

0.135

AC XY:

18337

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.472

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.0107

Gnomad SAS exome

AF:

0.0834

Gnomad FIN exome

AF:

0.166

Gnomad NFE exome

AF:

0.144

Gnomad OTH exome

AF:

0.150

GnomAD4 exome

AF:

0.141

AC:

205483

AN:

1457566

Hom.:

17481

Cov.:

AF XY:

0.139

AC XY:

100565

AN XY:

725442

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.109

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.00990

Gnomad4 SAS exome

AF:

0.0876

Gnomad4 FIN exome

AF:

0.164

Gnomad4 NFE exome

AF:

0.140

Gnomad4 OTH exome

AF:

0.151

GnomAD4 genome

AF:

0.227

AC:

34540

AN:

151860

Hom.:

5602

Cov.:

AF XY:

0.224

AC XY:

16595

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.160

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.0129

Gnomad4 SAS

AF:

0.0772

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.135

Hom.:

1206

Bravo

AF:

0.237

TwinsUK

AF:

0.135

AC:

502

ALSPAC

AF:

0.130

AC:

501

ESP6500AA

AF:

0.460

AC:

2026

ESP6500EA

AF:

0.145

AC:

1251

ExAC

AF:

0.150

AC:

18257

Asia WGS

AF:

0.0800

AC:

276

AN:

3478

EpiCase

AF:

0.143

EpiControl

AF:

0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.12

DANN

Benign

0.64

DEOGEN2

Benign

0.0010

.;T;.;.;.;.

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.068

LIST_S2

Benign

0.68

T;T;T;T;T;T

MetaRNN

Benign

0.00042

T;T;T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.0

N;N;N;N;N;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.40

PROVEAN

Benign

0.42

N;N;N;N;N;N

REVEL

Benign

0.019

Sift

Benign

0.19

T;T;T;T;T;T

Sift4G

Benign

0.21

T;T;T;T;T;T

Polyphen

0.73

P;B;.;.;.;.

Vest4

0.12

MutPred

0.29

Gain of catalytic residue at L23 (P = 0);Gain of catalytic residue at L23 (P = 0);Gain of catalytic residue at L23 (P = 0);Gain of catalytic residue at L23 (P = 0);Gain of catalytic residue at L23 (P = 0);.;

MPC

0.23

ClinPred

0.0076

GERP RS

-3.0

Varity_R

0.039

gMVP

0.14

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over