NM_004120.5:c.1150-441G>A

Variant names:

• chr1-89113125-C-T
• rs4656095
• NM_004120.5:c.1150-441G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004120.5(GBP2):​c.1150-441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 172,160 control chromosomes in the GnomAD database, including 46,254 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 0.73 (41275 hom., cov: 32)
  • Exomes 𝑓: 0.70 (4979 hom.)
• Consequence: GBP2 NM_004120.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 5 publications found

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]

ENSG00000307222 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GBP2	NM_004120.5	c.1150-441G>A		intron_variant	Intron 7 of 10	ENST00000370466.4	NP_004111.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GBP2	ENST00000370466.4	c.1150-441G>A		intron_variant	Intron 7 of 10	1	NM_004120.5	ENSP00000359497.3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111616 AN: 151996 Hom.: 41235 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.712

GnomAD4 exome AF: 0.696 AC: 13957 AN: 20046 Hom.: 4979 AF XY: 0.691 AC XY: 7073 AN XY: 10236

African (AFR) AF: 0.828 AC: 240 AN: 290

American (AMR) AF: 0.707 AC: 1363 AN: 1928

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 278 AN: 424

East Asian (EAS) AF: 0.804 AC: 756 AN: 940

South Asian (SAS) AF: 0.681 AC: 1403 AN: 2060

European-Finnish (FIN) AF: 0.761 AC: 496 AN: 652

Middle Eastern (MID) AF: 0.655 AC: 38 AN: 58

European-Non Finnish (NFE) AF: 0.684 AC: 8631 AN: 12616

Other (OTH) AF: 0.698 AC: 752 AN: 1078

GnomAD4 genome AF: 0.734 AC: 111712 AN: 152114 Hom.: 41275 Cov.: 32 AF XY: 0.737 AC XY: 54804 AN XY: 74378

African (AFR) AF: 0.801 AC: 33256 AN: 41502

American (AMR) AF: 0.703 AC: 10728 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3466

East Asian (EAS) AF: 0.799 AC: 4135 AN: 5174

South Asian (SAS) AF: 0.700 AC: 3375 AN: 4824

European-Finnish (FIN) AF: 0.812 AC: 8599 AN: 10588

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47153 AN: 67976

Other (OTH) AF: 0.714 AC: 1505 AN: 2108

Alfa AF: 0.732 Hom.: 5301

Bravo AF: 0.728

Asia WGS AF: 0.755 AC: 2628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.076
DANN	Benign	0.27
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4656095; hg19: chr1-89578808; COSMIC: COSV65068831; COSMIC: COSV65068831;