rs11052877

Positions:

• chr12-9753094-A-G

Variant summary

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

The NM_001781.2(CD69):​c.*387T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 153,716 control chromosomes in the GnomAD database, including 9,201 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 (9083 hom., cov: 32)
  • Exomes 𝑓: 0.37 (118 hom.)
• Consequence: CD69 NM_001781.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

CD69 (HGNC:1694): (CD69 molecule) This gene encodes a member of the calcium dependent lectin superfamily of type II transmembrane receptors. Expression of the encoded protein is induced upon activation of T lymphocytes, and may play a role in proliferation. Furthermore, the protein may act to transmit signals in natural killer cells and platelets. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD69	NM_001781.2	c.*387T>C		3_prime_UTR_variant	5/5	ENST00000228434.7	NP_001772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD69	ENST00000228434.7	c.*387T>C		3_prime_UTR_variant	5/5	1	NM_001781.2	ENSP00000228434.3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51353 AN: 151918 Hom.: 9083 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.367 AC: 616 AN: 1680 Hom.: 118 Cov.: 0 AF XY: 0.374 AC XY: 335 AN XY: 896

Gnomad4 AFR exome AF: 0.173

Gnomad4 AMR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.313

Gnomad4 FIN exome AF: 0.429

Gnomad4 NFE exome AF: 0.355

Gnomad4 OTH exome AF: 0.319

GnomAD4 genome AF: 0.338 AC: 51373 AN: 152036 Hom.: 9083 Cov.: 32 AF XY: 0.343 AC XY: 25497 AN XY: 74302

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.367

Alfa AF: 0.366 Hom.: 13986

Bravo AF: 0.324

Asia WGS AF: 0.368 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.5
DANN	Benign	0.76

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: rs11052877; hg19: chr12-9905690; COSMIC: COSV57303746; COSMIC: COSV57303746;