rs4763879

Variant names:

• chr12-9757568-G-A
• rs4763879
• NM_001781.2:c.65-1149C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001781.2(CD69):​c.65-1149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,822 control chromosomes in the GnomAD database, including 7,594 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 0.29 (7594 hom., cov: 32)
• Consequence: CD69 NM_001781.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 85 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD69	NM_001781.2	c.65-1149C>T		intron_variant	Intron 1 of 4	ENST00000228434.7	NP_001772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD69	ENST00000228434.7	c.65-1149C>T		intron_variant	Intron 1 of 4	1	NM_001781.2	ENSP00000228434.3
CD69	ENST00000536709.1	c.65-1149C>T		intron_variant	Intron 1 of 3	2		ENSP00000442597.1
CD69	ENST00000416624.6	n.146-1149C>T		intron_variant	Intron 1 of 2	2
CD69	ENST00000543147.1	n.146-1149C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43996 AN: 151704 Hom.: 7592 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 44001 AN: 151822 Hom.: 7594 Cov.: 32 AF XY: 0.292 AC XY: 21640 AN XY: 74172

African (AFR) AF: 0.0967 AC: 4004 AN: 41390

American (AMR) AF: 0.368 AC: 5614 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2338 AN: 5164

South Asian (SAS) AF: 0.387 AC: 1859 AN: 4804

European-Finnish (FIN) AF: 0.330 AC: 3452 AN: 10476

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24866 AN: 67948

Other (OTH) AF: 0.308 AC: 648 AN: 2104

Alfa AF: 0.345 Hom.: 41599

Bravo AF: 0.288

Asia WGS AF: 0.436 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.44
PhyloP100		-1.3
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: rs4763879; hg19: chr12-9910164;