dbSNP rs11052877: CD69:c.*387T>C (chr12-9753094-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

Publications

53 publications found

Variant links:

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]

CD69 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001781.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD69	NM_001781.2	MANE Select	c.*387T>C		3_prime_UTR	Exon 5 of 5	NP_001772.1	Q53ZX0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD69	ENST00000228434.7	TSL:1 MANE Select	c.*387T>C		3_prime_UTR	Exon 5 of 5	ENSP00000228434.3	Q07108

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51353

AN:

151918

Hom.:

9083

Cov.:

show subpopulations

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.:

AF XY:

0.374

AC XY:

335

AN XY:

896

show subpopulations

African (AFR)

AF:

0.173

AC:

AN:

American (AMR)

AF:

0.417

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.292

AC:

AN:

South Asian (SAS)

AF:

0.313

AC:

AN:

European-Finnish (FIN)

AF:

0.429

AC:

200

AN:

466

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.355

AC:

326

AN:

918

Other (OTH)

AF:

0.319

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.338

AC:

51373

AN:

152036

Hom.:

9083

Cov.:

AF XY:

0.343

AC XY:

25497

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.242

AC:

10041

AN:

41510

American (AMR)

AF:

0.336

AC:

5136

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

1650

AN:

3470

East Asian (EAS)

AF:

0.376

AC:

1943

AN:

5164

South Asian (SAS)

AF:

0.431

AC:

2078

AN:

4820

European-Finnish (FIN)

AF:

0.432

AC:

4562

AN:

10550

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.364

AC:

24747

AN:

67938

Other (OTH)

AF:

0.367

AC:

774

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1731

3462

5194

6925

8656

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.358

Hom.:

18395

Bravo

AF:

0.324

Asia WGS

AF:

0.368

AC:

1284

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.5

(source)

DANN

Benign

0.76

PhyloP100

0.059

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over