Variant 12-9753550-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001781.2(CD69):c.531A>G(p.Lys177Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00601 in 1,589,790 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0061 ( 54 hom. )

Consequence

CD69
NM_001781.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.79

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 made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 12-9753550-T-C is Benign according to our data. Variant chr12-9753550-T-C is described in ClinVar as [Benign]. Clinvar id is 769384.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.79 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD69	NM_001781.2 linkuse as main transcript	c.531A>G	p.Lys177Lys	synonymous_variant	5/5	ENST00000228434.7	NP_001772.1	Q07108Q53ZX0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD69	ENST00000228434.7 linkuse as main transcript	c.531A>G	p.Lys177Lys	synonymous_variant	5/5	1	NM_001781.2	ENSP00000228434.3		Q07108

Frequencies

GnomAD3 genomes

AF:

0.00526

AC:

801

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00973

Gnomad FIN

AF:

0.00848

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00782

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00576

AC:

1413

AN:

245410

Hom.:

AF XY:

0.00615

AC XY:

817

AN XY:

132862

show subpopulations

Gnomad AFR exome

AF:

0.00157

Gnomad AMR exome

AF:

0.00149

Gnomad ASJ exome

AF:

0.000400

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.00723

Gnomad FIN exome

AF:

0.00932

Gnomad NFE exome

AF:

0.00779

Gnomad OTH exome

AF:

0.00830

GnomAD4 exome

AF:

0.00609

AC:

8748

AN:

1437484

Hom.:

Cov.:

AF XY:

0.00619

AC XY:

4433

AN XY:

716302

show subpopulations

Gnomad4 AFR exome

AF:

0.00107

Gnomad4 AMR exome

AF:

0.00189

Gnomad4 ASJ exome

AF:

0.000308

Gnomad4 EAS exome

AF:

0.0000509

Gnomad4 SAS exome

AF:

0.00751

Gnomad4 FIN exome

AF:

0.00982

Gnomad4 NFE exome

AF:

0.00651

Gnomad4 OTH exome

AF:

0.00554

GnomAD4 genome

AF:

0.00526

AC:

801

AN:

152306

Hom.:

Cov.:

AF XY:

0.00526

AC XY:

392

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00418

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00974

Gnomad4 FIN

AF:

0.00848

Gnomad4 NFE

AF:

0.00782

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00568

Hom.:

Bravo

AF:

0.00422

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.55

DANN

Benign

0.34

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over