chr12-9699333-C-A

Position:

• chr12-9699333-C-A

Variant summary

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

The NM_013269.6(CLEC2D):​c.*4459C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,992 control chromosomes in the GnomAD database, including 10,560 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 0.34 (10560 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CLEC2D NM_013269.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC2D	NM_013269.6	c.*4459C>A		3_prime_UTR_variant	5/5	ENST00000290855.11	NP_037401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC2D	ENST00000290855.11	c.*4459C>A		3_prime_UTR_variant	5/5	1	NM_013269.6	ENSP00000290855	P2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51813 AN: 151874 Hom.: 10559 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.367

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.341 AC: 51816 AN: 151992 Hom.: 10560 Cov.: 32 AF XY: 0.342 AC XY: 25412 AN XY: 74264

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.373

Alfa AF: 0.419 Hom.: 17570

Bravo AF: 0.339

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs1044771; hg19: chr12-9851929;