rs7310460

chr12-9688177-T-A

Variant summary

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

The NM_013269.6(CLEC2D):c.357+91T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 1,277,960 control chromosomes in the GnomAD database, including 116,230 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 (10815 hom., cov: 29)
  • Exomes 𝑓: 0.43 (105415 hom.)
• Consequence: CLEC2D NM_013269.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC2D	NM_013269.6	c.357+91T>A		intron_variant		ENST00000290855.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC2D	ENST00000290855.11	c.357+91T>A		intron_variant		1	NM_013269.6	P2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 52793 AN: 149010 Hom.: 10815 Cov.: 29

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.427 AC: 482043 AN: 1128840 Hom.: 105415 Cov.: 22 AF XY: 0.427 AC XY: 232708 AN XY: 544726

Gnomad4 AFR exome AF: 0.129

Gnomad4 AMR exome AF: 0.519

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.615

Gnomad4 SAS exome AF: 0.395

Gnomad4 FIN exome AF: 0.420

Gnomad4 NFE exome AF: 0.430

Gnomad4 OTH exome AF: 0.415

GnomAD4 genome AF: 0.354 AC: 52809 AN: 149120 Hom.: 10815 Cov.: 29 AF XY: 0.355 AC XY: 25721 AN XY: 72524

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.391

Alfa AF: 0.396 Hom.: 1622

Bravo AF: 0.356

Asia WGS AF: 0.490 AC: 1701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.1
Dann	Benign	0.68

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: rs7310460; hg19: chr12-9840773;