Variant chr12-6800214-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000616.5(CD4):c.49+28del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 24846 hom., cov: 0)

Exomes 𝑓: 0.62 ( 285692 hom. )

Consequence

CD4
NM_000616.5 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.358

Variant links:

Genes affected

CD4 (HGNC:1678): (CD4 molecule) This gene encodes the CD4 membrane glycoprotein of T lymphocytes. The CD4 antigen acts as a coreceptor with the T-cell receptor on the T lymphocyte to recognize antigens displayed by an antigen presenting cell in the context of class II MHC molecules. The CD4 antigen is also a primary receptor for entry of the human immunodeficiency virus through interactions with the HIV Env gp120 subunit. This gene is expressed not only in T lymphocytes, but also in B cells, macrophages, granulocytes, as well as in various regions of the brain. The protein functions to initiate or augment the early phase of T-cell activation, and may function as an important mediator of indirect neuronal damage in infectious and immune-mediated diseases of the central nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, May 2020]

CD4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-6800214-TG-T is Benign according to our data. Variant chr12-6800214-TG-T is described in ClinVar as [Benign]. Clinvar id is 1192704.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD4	NM_000616.5 linkuse as main transcript	c.49+28del		intron_variant		ENST00000011653.9	NP_000607.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD4	ENST00000011653.9 linkuse as main transcript	c.49+28del		intron_variant		1	NM_000616.5	ENSP00000011653	P1

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85404

AN:

151358

Hom.:

24844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.551

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.612

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.647

Gnomad OTH

AF:

0.577

GnomAD3 exomes

AF:

0.581

AC:

146021

AN:

251130

Hom.:

43376

AF XY:

0.583

AC XY:

79121

AN XY:

135732

show subpopulations

Gnomad AFR exome

AF:

0.421

Gnomad AMR exome

AF:

0.505

Gnomad ASJ exome

AF:

0.565

Gnomad EAS exome

AF:

0.609

Gnomad SAS exome

AF:

0.474

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.646

Gnomad OTH exome

AF:

0.590

GnomAD4 exome

AF:

0.622

AC:

908737

AN:

1460290

Hom.:

285692

Cov.:

AF XY:

0.619

AC XY:

449460

AN XY:

726504

show subpopulations

Gnomad4 AFR exome

AF:

0.421

Gnomad4 AMR exome

AF:

0.504

Gnomad4 ASJ exome

AF:

0.566

Gnomad4 EAS exome

AF:

0.652

Gnomad4 SAS exome

AF:

0.476

Gnomad4 FIN exome

AF:

0.623

Gnomad4 NFE exome

AF:

0.647

Gnomad4 OTH exome

AF:

0.593

GnomAD4 genome

AF:

0.564

AC:

85447

AN:

151476

Hom.:

24846

Cov.:

AF XY:

0.563

AC XY:

41608

AN XY:

73944

show subpopulations

Gnomad4 AFR

AF:

0.425

Gnomad4 AMR

AF:

0.551

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.466

Gnomad4 FIN

AF:

0.612

Gnomad4 NFE

AF:

0.647

Gnomad4 OTH

AF:

0.577

Alfa

AF:

0.321

Hom.:

2695

Bravo

AF:

0.556

Asia WGS

AF:

0.514

AC:

1789

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 72% of patients studied by a panel of primary immunodeficiencies. Number of patients: 68. Only high quality variants are reported. -

Immunodeficiency 79

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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