rs1181388

Positions:

• chr2-203711228-A-G

Variant summary

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

The NM_006139.4(CD28):​c.52+4480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,120 control chromosomes in the GnomAD database, including 49,419 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 0.80 (49419 hom., cov: 31)
• Consequence: CD28 NM_006139.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

CD28 (HGNC:1653): (CD28 molecule) The protein encoded by this gene is essential for T-cell proliferation and survival, cytokine production, and T-helper type-2 development. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD28	NM_006139.4	c.52+4480A>G		intron_variant		ENST00000324106.9
CD28	NM_001243077.2	c.52+4480A>G		intron_variant
CD28	NM_001243078.2	c.52+4480A>G		intron_variant
CD28	NM_001410981.1	c.94+4611A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD28	ENST00000324106.9	c.52+4480A>G		intron_variant		1	NM_006139.4	P1
CD28	ENST00000374481.7	c.52+4480A>G		intron_variant		1
CD28	ENST00000458610.6	c.94+4611A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121902 AN: 152000 Hom.: 49407 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.802 AC: 121957 AN: 152120 Hom.: 49419 Cov.: 31 AF XY: 0.801 AC XY: 59549 AN XY: 74366

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.806

Alfa AF: 0.841 Hom.: 49217

Bravo AF: 0.788

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.79

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: rs1181388; hg19: chr2-204575951;