rs9332411

chr12-9681749-C-T

Variant summary

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

The NM_013269.6(CLEC2D):c.172+716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,992 control chromosomes in the GnomAD database, including 10,919 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 0.35 (10919 hom., cov: 32)
• Consequence: CLEC2D NM_013269.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC2D	NM_013269.6	c.172+716C>T		intron_variant		ENST00000290855.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC2D	ENST00000290855.11	c.172+716C>T		intron_variant		1	NM_013269.6	P2

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53845 AN: 151874 Hom.: 10919 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.386

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53862 AN: 151992 Hom.: 10919 Cov.: 32 AF XY: 0.356 AC XY: 26439 AN XY: 74286

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.392

Alfa AF: 0.380 Hom.: 2179

Bravo AF: 0.354

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.4
Dann	Benign	0.58

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: rs9332411; hg19: chr12-9834345;