chr12-9681749-C-T

Variant names:

• chr12-9681749-C-T
• rs9332411
• NM_013269.6:c.172+716C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013269.6. 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
	CLEC2D	NM_013269.6	MANE Select	c.172+716C>T		intron	N/A	NP_037401.1
	CLEC2D	NM_001004419.5		c.172+716C>T		intron	N/A	NP_001004419.1
	CLEC2D	NM_001197317.3		c.62-6153C>T		intron	N/A	NP_001184246.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC2D	ENST00000290855.11	TSL:1 MANE Select	c.172+716C>T		intron	N/A	ENSP00000290855.6
	CLEC2D	ENST00000261340.11	TSL:1	c.172+716C>T		intron	N/A	ENSP00000261340.7
	CLEC2D	ENST00000430909.5	TSL:1	c.109+716C>T		intron	N/A	ENSP00000413045.1

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

African (AFR) AF: 0.150 AC: 6223 AN: 41476

American (AMR) AF: 0.431 AC: 6580 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1331 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2895 AN: 5182

South Asian (SAS) AF: 0.409 AC: 1971 AN: 4814

European-Finnish (FIN) AF: 0.388 AC: 4086 AN: 10528

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29420 AN: 67936

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.374 Hom.: 2187

Bravo AF: 0.354

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.58
PhyloP100		0.82
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9332411; hg19: chr12-9834345;