dbSNP rs928655: GBP6:c.1469-78G>A (chr1-89384015-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198460.3(GBP6):c.1469-78G>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 1,371,602 control chromosomes in the GnomAD database, including 372,240 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 0.66 ( 34902 hom., cov: 33)

Exomes 𝑓: 0.74 ( 337338 hom. )

Consequence

GBP6
NM_198460.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.642

Publications

25 publications found

Variant links:

Genes affected

GBP6 (HGNC:25395): (guanylate binding protein family member 6) Guanylate-binding proteins, such as GBP6, are induced by interferon and hydrolyze GTP to both GDP and GMP (Olszewski et al., 2006 [PubMed 16689661]).[supplied by OMIM, Dec 2008]

GBP6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GBP6	NM_198460.3 link	c.1469-78G>A	intron_variant	Intron 9 of 10	ENST00000370456.5	NP_940862.2	Q6ZN66-1
GBP6	NM_001320257.2 link	c.1079-78G>A	intron_variant	Intron 7 of 8		NP_001307186.1	B4E1U2B4DRX0
GBP6	XM_011540835.4 link	c.1469-78G>A	intron_variant	Intron 9 of 10		XP_011539137.1	Q6ZN66-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GBP6	ENST00000370456.5 link	c.1469-78G>A		intron_variant	Intron 9 of 10	1	NM_198460.3	ENSP00000359485.5		Q6ZN66-1

Frequencies

GnomAD3 genomes

AF:

0.664

AC:

100985

AN:

152004

Hom.:

34898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.825

Gnomad AMR

AF:

0.647

Gnomad ASJ

AF:

0.839

Gnomad EAS

AF:

0.350

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.739

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.683

GnomAD4 exome

AF:

0.738

AC:

899766

AN:

1219480

Hom.:

337338

AF XY:

0.738

AC XY:

442891

AN XY:

600414

show subpopulations

African (AFR)

AF:

0.494

AC:

13398

AN:

27108

American (AMR)

AF:

0.617

AC:

13678

AN:

22172

Ashkenazi Jewish (ASJ)

AF:

0.834

AC:

15654

AN:

18766

East Asian (EAS)

AF:

0.342

AC:

12261

AN:

35866

South Asian (SAS)

AF:

0.656

AC:

40874

AN:

62282

European-Finnish (FIN)

AF:

0.742

AC:

35111

AN:

47296

Middle Eastern (MID)

AF:

0.777

AC:

3262

AN:

4200

European-Non Finnish (NFE)

AF:

0.767

AC:

728899

AN:

950506

Other (OTH)

AF:

0.714

AC:

36629

AN:

51284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

10836

21673

32509

43346

54182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17342

34684

52026

69368

86710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.664

AC:

101015

AN:

152122

Hom.:

34902

Cov.:

AF XY:

0.661

AC XY:

49187

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.501

AC:

20774

AN:

41488

American (AMR)

AF:

0.648

AC:

9893

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.839

AC:

2912

AN:

3472

East Asian (EAS)

AF:

0.350

AC:

1807

AN:

5156

South Asian (SAS)

AF:

0.642

AC:

3099

AN:

4826

European-Finnish (FIN)

AF:

0.739

AC:

7819

AN:

10574

Middle Eastern (MID)

AF:

0.752

AC:

221

AN:

294

European-Non Finnish (NFE)

AF:

0.769

AC:

52307

AN:

68016

Other (OTH)

AF:

0.678

AC:

1431

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1648

3297

4945

6594

8242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.731

Hom.:

183129

Bravo

AF:

0.649

Asia WGS

AF:

0.468

AC:

1628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.052

(source)

DANN

Benign

0.50

PhyloP100

-0.64

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over