1-89106292-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004120.5(GBP2):​c.*1883G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,048 control chromosomes in the GnomAD database, including 41,676 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 0.74 ( 41675 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

GBP2
NM_004120.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547
Variant links:
Genes affected
GBP2 (HGNC:4183): (guanylate binding protein 2) This gene belongs to the guanine-binding protein (GBP) family, which includes interferon-induced proteins that can bind to guanine nucleotides (GMP, GDP and GTP). The encoded protein is a GTPase which hydrolyzes GTP, predominantly to GDP. The protein may play a role as a marker of squamous cell carcinomas. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GBP2NM_004120.5 linkuse as main transcriptc.*1883G>A 3_prime_UTR_variant 11/11 ENST00000370466.4 NP_004111.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GBP2ENST00000370466.4 linkuse as main transcriptc.*1883G>A 3_prime_UTR_variant 11/111 NM_004120.5 ENSP00000359497 P1
GBP2ENST00000464839.5 linkuse as main transcriptc.*913G>A 3_prime_UTR_variant, NMD_transcript_variant 15/152 ENSP00000434282

Frequencies

GnomAD3 genomes
AF:
0.738
AC:
112079
AN:
151928
Hom.:
41627
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.815
Gnomad AMI
AF:
0.590
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.635
Gnomad EAS
AF:
0.793
Gnomad SAS
AF:
0.700
Gnomad FIN
AF:
0.812
Gnomad MID
AF:
0.731
Gnomad NFE
AF:
0.694
Gnomad OTH
AF:
0.715
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AF XY:
1.00
AC XY:
2
AN XY:
2
show subpopulations
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.738
AC:
112183
AN:
152046
Hom.:
41675
Cov.:
32
AF XY:
0.740
AC XY:
54999
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.815
Gnomad4 AMR
AF:
0.703
Gnomad4 ASJ
AF:
0.635
Gnomad4 EAS
AF:
0.794
Gnomad4 SAS
AF:
0.700
Gnomad4 FIN
AF:
0.812
Gnomad4 NFE
AF:
0.694
Gnomad4 OTH
AF:
0.717
Alfa
AF:
0.726
Hom.:
5538
Bravo
AF:
0.733
Asia WGS
AF:
0.755
AC:
2623
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.5
DANN
Benign
0.80

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: rs4656093; hg19: chr1-89571975; API