rs679982

Variant summary

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

The ENST00000398937.6(CLEC1B):​c.267-4140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,052 control chromosomes in the GnomAD database, including 26,129 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 0.58 ( 26129 hom., cov: 32)

Consequence

CLEC1B
ENST00000398937.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.532
Variant links:
Genes affected
CLEC1B (HGNC:24356): (C-type lectin domain family 1 member B) Natural killer (NK) cells express multiple calcium-dependent (C-type) lectin-like receptors, such as CD94 (KLRD1; MIM 602894) and NKG2D (KLRC4; MIM 602893), that interact with major histocompatibility complex class I molecules and either inhibit or activate cytotoxicity and cytokine secretion. CLEC2 is a C-type lectin-like receptor expressed in myeloid cells and NK cells (Colonna et al., 2000 [PubMed 10671229]).[supplied by OMIM, Jan 2011]
CLEC12A (HGNC:31713): (C-type lectin domain family 12 member A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The protein encoded by this gene is a negative regulator of granulocyte and monocyte function. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. This gene is closely linked to other CTL/CTLD superfamily members in the natural killer gene complex region on chromosome 12p13. [provided by RefSeq, May 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=-1.04).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLEC12AXM_006719035.4 linkuse as main transcriptc.642-4720G>A intron_variant
CLEC12AXM_011520573.3 linkuse as main transcriptc.642-4723G>A intron_variant
CLEC12AXM_047428399.1 linkuse as main transcriptc.672-4720G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLEC1BENST00000398937.6 linkuse as main transcriptc.267-4140C>T intron_variant 3
CLEC12AENST00000449959.6 linkuse as main transcriptn.1005-4720G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.581
AC:
88203
AN:
151934
Hom.:
26104
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.585
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.584
Gnomad ASJ
AF:
0.568
Gnomad EAS
AF:
0.873
Gnomad SAS
AF:
0.795
Gnomad FIN
AF:
0.514
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.570
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.581
AC:
88277
AN:
152052
Hom.:
26129
Cov.:
32
AF XY:
0.585
AC XY:
43510
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.585
Gnomad4 AMR
AF:
0.584
Gnomad4 ASJ
AF:
0.568
Gnomad4 EAS
AF:
0.873
Gnomad4 SAS
AF:
0.795
Gnomad4 FIN
AF:
0.514
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.575
Alfa
AF:
0.556
Hom.:
4004
Bravo
AF:
0.579
Asia WGS
AF:
0.791
AC:
2748
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.48
DANN
Benign
0.11

Splicing

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.

Other links and lift over

dbSNP: rs679982; hg19: chr12-10142897; API