Variant chr1-89191291-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_052941.5(GBP4):c.886C>T(p.Leu296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0091 in 1,613,772 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0092 ( 86 hom. )

Consequence

GBP4
NM_052941.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.224

Variant links:

Genes affected

GBP4 (HGNC:20480): (guanylate binding protein 4) Guanylate-binding proteins, such as GBP4, are induced by interferon and hydrolyze GTP to both GDP and GMP (Vestal, 2005 [PubMed 16108726]).[supplied by OMIM, Dec 2008]

GBP4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 1-89191291-G-A is Benign according to our data. Variant chr1-89191291-G-A is described in ClinVar as [Benign]. Clinvar id is 781583.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.224 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00924 (13498/1461472) while in subpopulation MID AF= 0.0248 (143/5768). AF 95% confidence interval is 0.0215. There are 86 homozygotes in gnomad4_exome. There are 6703 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBP4	NM_052941.5 linkuse as main transcript	c.886C>T	p.Leu296=	synonymous_variant	6/11	ENST00000355754.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBP4	ENST00000355754.7 linkuse as main transcript	c.886C>T	p.Leu296=	synonymous_variant	6/11	1	NM_052941.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00783

AC:

1192

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00171

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0166

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.000849

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0110

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.00775

AC:

1948

AN:

251392

Hom.:

AF XY:

0.00801

AC XY:

1088

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00937

Gnomad ASJ exome

AF:

0.0129

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.00634

Gnomad FIN exome

AF:

0.00106

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.0127

GnomAD4 exome

AF:

0.00924

AC:

13498

AN:

1461472

Hom.:

Cov.:

AF XY:

0.00922

AC XY:

6703

AN XY:

726970

show subpopulations

Gnomad4 AFR exome

AF:

0.00191

Gnomad4 AMR exome

AF:

0.00997

Gnomad4 ASJ exome

AF:

0.0127

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.00661

Gnomad4 FIN exome

AF:

0.00142

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.0104

GnomAD4 genome

AF:

0.00782

AC:

1191

AN:

152300

Hom.:

Cov.:

AF XY:

0.00712

AC XY:

530

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00171

Gnomad4 AMR

AF:

0.0166

Gnomad4 ASJ

AF:

0.0104

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.000849

Gnomad4 NFE

AF:

0.0110

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.00957

Hom.:

Bravo

AF:

0.00926

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0110

EpiControl

AF:

0.0126

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

1.2

DANN

Benign

0.48

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over