rs1054611

chr12-10017562-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000396502.5(CLEC12B):c.*1816G>T variant causes a 3 prime UTR 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 ENST00000396502.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC12B	NM_001129998.3	c.681-769G>T		intron_variant		ENST00000338896.11
LOC102724020	NR_169587.1	n.258-1414C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC12B	ENST00000338896.11	c.681-769G>T		intron_variant		1	NM_001129998.3	P1
	ENST00000544225.1	n.249-1789C>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR exome AF: 0.498

Gnomad4 AMR exome AF: 0.524

Gnomad4 ASJ exome AF: 0.432

Gnomad4 EAS exome AF: 0.804

Gnomad4 SAS exome AF: 0.628

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.409

Gnomad4 OTH exome AF: 0.466

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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.470

Alfa AF: 0.431 Hom.: 11173

Bravo AF: 0.468

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.45
Dann	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs1054611; hg19: chr12-10170161;