ENST00000539155.1:n.*2309G>T

Variant names:

• chr12-10017562-G-T
• rs1054611
• ENST00000539155.1:n.*2309G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539155.1(CLEC12B):​n.*2309G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 985,062 control chromosomes in the GnomAD database, including 91,079 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 0.46 (16608 hom., cov: 32)
  • Exomes 𝑓: 0.42 (74471 hom.)
• Consequence: CLEC12B ENST00000539155.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 12 publications found

Genes affected

CLEC12B (HGNC:31966): (C-type lectin domain family 12 member B) Enables protein phosphatase binding activity and signaling receptor inhibitor activity. Involved in natural killer cell inhibitory signaling pathway; negative regulation of natural killer cell mediated cytotoxicity; and negative regulation of signaling receptor activity. Located in external side of plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000256803 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539155.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC12B	NM_001129998.3	MANE Select	c.681-769G>T		intron	N/A	NP_001123470.1
	CLEC12B	NM_205852.3		c.*1816G>T		3_prime_UTR	Exon 5 of 5	NP_995324.2
	CLEC12B	NM_001319242.1		c.*1816G>T		3_prime_UTR	Exon 5 of 5	NP_001306171.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC12B	ENST00000539155.1	TSL:1	n.*2309G>T		non_coding_transcript_exon	Exon 5 of 5	ENSP00000444909.1
	CLEC12B	ENST00000396502.5	TSL:1	c.*1816G>T		3_prime_UTR	Exon 5 of 5	ENSP00000379759.1
	CLEC12B	ENST00000539155.1	TSL:1	n.*2309G>T		3_prime_UTR	Exon 5 of 5	ENSP00000444909.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69958 AN: 151844 Hom.: 16582 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.463

GnomAD4 exome AF: 0.419 AC: 349330 AN: 833100 Hom.: 74471 Cov.: 33 AF XY: 0.419 AC XY: 161009 AN XY: 384714

African (AFR) AF: 0.498 AC: 7862 AN: 15780

American (AMR) AF: 0.524 AC: 516 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 2224 AN: 5152

East Asian (EAS) AF: 0.804 AC: 2920 AN: 3632

South Asian (SAS) AF: 0.628 AC: 10344 AN: 16460

European-Finnish (FIN) AF: 0.385 AC: 134 AN: 348

Middle Eastern (MID) AF: 0.444 AC: 719 AN: 1620

European-Non Finnish (NFE) AF: 0.409 AC: 311885 AN: 761826

Other (OTH) AF: 0.466 AC: 12726 AN: 27298

GnomAD4 genome AF: 0.461 AC: 70024 AN: 151962 Hom.: 16608 Cov.: 32 AF XY: 0.467 AC XY: 34697 AN XY: 74266

African (AFR) AF: 0.497 AC: 20609 AN: 41448

American (AMR) AF: 0.506 AC: 7716 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4127 AN: 5160

South Asian (SAS) AF: 0.653 AC: 3142 AN: 4812

European-Finnish (FIN) AF: 0.368 AC: 3883 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27435 AN: 67968

Other (OTH) AF: 0.470 AC: 993 AN: 2114

Alfa AF: 0.430 Hom.: 12936

Bravo AF: 0.468

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1054611; hg19: chr12-10170161;