chr2-203864430-C-T

Position:

• chr2-203864430-C-T

Variant summary

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

The ENST00000696479.1(CTLA4):​c.48-3488C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,984 control chromosomes in the GnomAD database, including 13,645 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 0.42 (13645 hom., cov: 32)
• Consequence: CTLA4 ENST00000696479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

Genes affected

CTLA4 (HGNC:2505): (cytotoxic T-lymphocyte associated protein 4) This gene is a member of the immunoglobulin superfamily and encodes a protein which transmits an inhibitory signal to T cells. The protein contains a V domain, a transmembrane domain, and a cytoplasmic tail. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. The membrane-bound isoform functions as a homodimer interconnected by a disulfide bond, while the soluble isoform functions as a monomer. Mutations in this gene have been associated with insulin-dependent diabetes mellitus, Graves disease, Hashimoto thyroiditis, celiac disease, systemic lupus erythematosus, thyroid-associated orbitopathy, and other autoimmune diseases. [provided by RefSeq, Jul 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTLA4	ENST00000696479.1	c.48-3488C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63405 AN: 151866 Hom.: 13628 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.418 AC: 63467 AN: 151984 Hom.: 13645 Cov.: 32 AF XY: 0.423 AC XY: 31415 AN XY: 74288

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.379

Alfa AF: 0.418 Hom.: 1884

Bravo AF: 0.413

Asia WGS AF: 0.448 AC: 1553 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	3.0
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs231770; hg19: chr2-204729153;