rs149914857

Positions:

chr1-92481068-G-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005263.5(GFI1):c.319C>G(p.Pro107Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 1,611,614 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P107P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., cov: 34)

Exomes 𝑓: 0.0039 ( 13 hom. )

Consequence

GFI1
NM_005263.5 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 7.36

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008533537).

BP6

Variant 1-92481068-G-C is Benign according to our data. Variant chr1-92481068-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 259703.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-92481068-G-C is described in Lovd as [Likely_benign].

BS2

High AC in GnomAd4 at 395 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GFI1	NM_005263.5 linkuse as main transcript	c.319C>G	p.Pro107Ala	missense_variant	4/7	ENST00000294702.6	NP_005254.2	Q99684

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GFI1	ENST00000294702.6 linkuse as main transcript	c.319C>G	p.Pro107Ala	missense_variant	4/7	2	NM_005263.5	ENSP00000294702.5	Q99684
GFI1	ENST00000370332.5 linkuse as main transcript	c.319C>G	p.Pro107Ala	missense_variant	4/7	1		ENSP00000359357.1	Q99684
GFI1	ENST00000427103.6 linkuse as main transcript	c.319C>G	p.Pro107Ala	missense_variant	4/7	1		ENSP00000399719.1	Q99684

Frequencies

GnomAD3 genomes

AF:

0.00260

AC:

395

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000941

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00454

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00221

AC:

530

AN:

239476

Hom.:

AF XY:

0.00230

AC XY:

301

AN XY:

130642

show subpopulations

Gnomad AFR exome

AF:

0.00122

Gnomad AMR exome

AF:

0.00248

Gnomad ASJ exome

AF:

0.00225

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000791

Gnomad FIN exome

AF:

0.000675

Gnomad NFE exome

AF:

0.00328

Gnomad OTH exome

AF:

0.00374

GnomAD4 exome

AF:

0.00395

AC:

5764

AN:

1459288

Hom.:

Cov.:

AF XY:

0.00387

AC XY:

2811

AN XY:

726014

show subpopulations

Gnomad4 AFR exome

AF:

0.000839

Gnomad4 AMR exome

AF:

0.00235

Gnomad4 ASJ exome

AF:

0.00223

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000917

Gnomad4 FIN exome

AF:

0.000988

Gnomad4 NFE exome

AF:

0.00467

Gnomad4 OTH exome

AF:

0.00390

GnomAD4 genome

AF:

0.00259

AC:

395

AN:

152326

Hom.:

Cov.:

AF XY:

0.00247

AC XY:

184

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00124

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000941

Gnomad4 NFE

AF:

0.00454

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00343

Hom.:

Bravo

AF:

0.00241

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00221

AC:

ExAC

AF:

0.00232

AC:

279

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00356

ClinVar

Significance: Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2023	GFI1: BP4, BS2 -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not specified

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jan 19, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Neutropenia, severe congenital, 2, autosomal dominant

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.57

D;D;D

Eigen

Benign

0.11

Eigen_PC

Uncertain

0.22

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.81

.;T;.

M_CAP

Benign

0.0064

MetaRNN

Benign

0.0085

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

M;M;M

PrimateAI

Benign

0.44

PROVEAN

Uncertain

-2.9

D;D;D

REVEL

Benign

0.11

Sift

Benign

0.13

T;T;T

Sift4G

Benign

0.068

T;T;T

Polyphen

0.0090

B;B;B

Vest4

0.24

MVP

0.79

MPC

1.4

ClinPred

0.026

GERP RS

4.4

Varity_R

0.087

gMVP

0.16

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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