rs34631763

Positions:

chr1-92483381-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005263.5(GFI1):c.107G>A(p.Ser36Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 1,602,830 control chromosomes in the GnomAD database, including 2,489 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 183 hom., cov: 33)

Exomes 𝑓: 0.052 ( 2306 hom. )

Consequence

GFI1
NM_005263.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7O:1

Conservation

PhyloP100: 2.50

Variant links:

Genes affected

GFI1 (HGNC:4237): (growth factor independent 1 transcriptional repressor) This gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters. Mutations in this gene cause autosomal dominant severe congenital neutropenia, and also dominant nonimmune chronic idiopathic neutropenia of adults, which are heterogeneous hematopoietic disorders that cause predispositions to leukemias and infections. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]

GFI1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018077791).

BP6

Variant 1-92483381-C-T is Benign according to our data. Variant chr1-92483381-C-T is described in ClinVar as [Benign]. Clinvar id is 259699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-92483381-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GFI1	NM_005263.5 linkuse as main transcript	c.107G>A	p.Ser36Asn	missense_variant	2/7	ENST00000294702.6	NP_005254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GFI1	ENST00000294702.6 linkuse as main transcript	c.107G>A	p.Ser36Asn	missense_variant	2/7	2	NM_005263.5	ENSP00000294702	P1

Frequencies

GnomAD3 genomes

AF:

0.0404

AC:

6151

AN:

152242

Hom.:

183

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0103

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0430

Gnomad ASJ

AF:

0.0651

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0585

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0592

Gnomad OTH

AF:

0.0431

GnomAD3 exomes

AF:

0.0397

AC:

9753

AN:

245864

Hom.:

261

AF XY:

0.0394

AC XY:

5267

AN XY:

133580

show subpopulations

Gnomad AFR exome

AF:

0.00945

Gnomad AMR exome

AF:

0.0282

Gnomad ASJ exome

AF:

0.0681

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00890

Gnomad FIN exome

AF:

0.0568

Gnomad NFE exome

AF:

0.0564

Gnomad OTH exome

AF:

0.0456

GnomAD4 exome

AF:

0.0521

AC:

75620

AN:

1450470

Hom.:

2306

Cov.:

AF XY:

0.0512

AC XY:

36943

AN XY:

722128

show subpopulations

Gnomad4 AFR exome

AF:

0.00743

Gnomad4 AMR exome

AF:

0.0292

Gnomad4 ASJ exome

AF:

0.0697

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00977

Gnomad4 FIN exome

AF:

0.0559

Gnomad4 NFE exome

AF:

0.0593

Gnomad4 OTH exome

AF:

0.0500

GnomAD4 genome

AF:

0.0404

AC:

6151

AN:

152360

Hom.:

183

Cov.:

AF XY:

0.0407

AC XY:

3030

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.0102

Gnomad4 AMR

AF:

0.0429

Gnomad4 ASJ

AF:

0.0651

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0106

Gnomad4 FIN

AF:

0.0585

Gnomad4 NFE

AF:

0.0592

Gnomad4 OTH

AF:

0.0426

Alfa

AF:

0.0545

Hom.:

389

Bravo

AF:

0.0369

TwinsUK

AF:

0.0663

AC:

246

ALSPAC

AF:

0.0589

AC:

227

ESP6500AA

AF:

0.0134

AC:

ESP6500EA

AF:

0.0545

AC:

469

ExAC

AF:

0.0377

AC:

4572

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.0552

EpiControl

AF:

0.0552

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Gene associated with congenital neutropaenia -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:2Other:1

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Neutropenia, severe congenital, 2, autosomal dominant

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.13

T;T;T

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.0087

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.45

.;T;.

MetaRNN

Benign

0.0018

T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.0

N;N;N

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.94

N;N;N

REVEL

Benign

0.057

Sift

Benign

0.063

T;T;T

Sift4G

Benign

0.50

T;T;T

Polyphen

0.026

B;B;B

Vest4

0.046

MPC

0.60

ClinPred

0.015

GERP RS

4.3

Varity_R

0.15

gMVP

0.062

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