NM_005214.5:c.*528_*571delATATATATATATATATATATATATATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_005214.5(CTLA4):​c.*528_*571delATATATATATATATATATATATATATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 181,422 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0036 ( 1 hom. )

Consequence

CTLA4
NM_005214.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.83
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000655 (8/122094) while in subpopulation AMR AF= 0.000244 (3/12288). AF 95% confidence interval is 0.0000664. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CTLA4NM_005214.5 linkc.*528_*571delATATATATATATATATATATATATATATATATATATATATATAT 3_prime_UTR_variant Exon 4 of 4 ENST00000648405.2 NP_005205.2 P16410-1
CTLA4NM_001037631.3 linkc.*565_*608delATATATATATATATATATATATATATATATATATATATATATAT 3_prime_UTR_variant Exon 3 of 3 NP_001032720.1 P16410-5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTLA4ENST00000648405.2 linkc.*528_*571delATATATATATATATATATATATATATATATATATATATATATAT 3_prime_UTR_variant Exon 4 of 4 NM_005214.5 ENSP00000497102.1 P16410-1
CTLA4ENST00000696479.1 linkc.*528_*571delATATATATATATATATATATATATATATATATATATATATATAT 3_prime_UTR_variant Exon 5 of 5 ENSP00000512655.1 A0A8Q3SIR7

Frequencies

GnomAD3 genomes
AF:
0.0000655
AC:
8
AN:
122102
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000677
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000244
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000172
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000334
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00357
AC:
212
AN:
59328
Hom.:
1
AF XY:
0.00371
AC XY:
111
AN XY:
29936
show subpopulations
Gnomad4 AFR exome
AF:
0.00259
Gnomad4 AMR exome
AF:
0.00415
Gnomad4 ASJ exome
AF:
0.00311
Gnomad4 EAS exome
AF:
0.00148
Gnomad4 SAS exome
AF:
0.00242
Gnomad4 FIN exome
AF:
0.00214
Gnomad4 NFE exome
AF:
0.00382
Gnomad4 OTH exome
AF:
0.00463
GnomAD4 genome
AF:
0.0000655
AC:
8
AN:
122094
Hom.:
0
Cov.:
0
AF XY:
0.0000515
AC XY:
3
AN XY:
58196
show subpopulations
Gnomad4 AFR
AF:
0.0000676
Gnomad4 AMR
AF:
0.000244
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000172
Gnomad4 NFE
AF:
0.0000334
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs60872763; hg19: chr2-204738050; API