Variant chr1-89117007-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004120.5(GBP2):c.853C>A(p.Pro285Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P285A) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

GBP2
NM_004120.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.864

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]

GBP2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06552246).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GBP2	NM_004120.5 linkuse as main transcript	c.853C>A	p.Pro285Thr	missense_variant	6/11	ENST00000370466.4	NP_004111.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
GBP2	ENST00000370466.4 linkuse as main transcript	c.853C>A	p.Pro285Thr	missense_variant	6/11	1	NM_004120.5	ENSP00000359497	P1
GBP2	ENST00000463660.1 linkuse as main transcript	n.2872C>A		non_coding_transcript_exon_variant	2/5	2
GBP2	ENST00000464839.5 linkuse as main transcript	c.853C>A	p.Pro285Thr	missense_variant, NMD_transcript_variant	9/15	2		ENSP00000434282

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.8

DANN

Benign

0.18

DEOGEN2

Benign

0.023

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00087

LIST_S2

Benign

0.10

M_CAP

Benign

0.0049

MetaRNN

Benign

0.066

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-2.1

MutationTaster

Benign

1.0

PrimateAI

Benign

0.26

PROVEAN

Benign

1.1

REVEL

Benign

0.043

Sift

Benign

0.70

Sift4G

Benign

0.54

Polyphen

0.0

Vest4

0.031

MutPred

0.28

Loss of loop (P = 0.1242);

MVP

0.12

MPC

0.11

ClinPred

0.034

GERP RS

-0.66

Varity_R

0.043

gMVP

0.099

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over