Variant chr9-132986611-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001377304.1(GFI1B):c.-20-48T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 886,946 control chromosomes in the GnomAD database, including 54,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7676 hom., cov: 32)

Exomes 𝑓: 0.35 ( 46610 hom. )

Consequence

GFI1B
NM_001377304.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.76

Variant links:

Genes affected

GFI1B (HGNC:4238): (growth factor independent 1B transcriptional repressor) This gene encodes a zinc-finger containing transcriptional regulator that is primarily expressed in cells of hematopoietic lineage. The encoded protein complexes with numerous other transcriptional regulatory proteins including GATA-1, runt-related transcription factor 1 and histone deacetylases to control expression of genes involved in the development and maturation of erythrocytes and megakaryocytes. Mutations in this gene are the cause of the autosomal dominant platelet disorder, platelet-type bleeding disorder-17. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

GFI1B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 9-132986611-T-G is Benign according to our data. Variant chr9-132986611-T-G is described in ClinVar as [Benign]. Clinvar id is 1261847.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFI1B	NM_001377304.1 linkuse as main transcript	c.-20-48T>G		intron_variant		ENST00000372122.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GFI1B	ENST00000372122.4 linkuse as main transcript	c.-20-48T>G	intron_variant	1	NM_001377304.1	P1	Q5VTD9-1
GFI1B	ENST00000339463.7 linkuse as main transcript	c.-20-48T>G	intron_variant	1		P1	Q5VTD9-1
GFI1B	ENST00000372123.5 linkuse as main transcript	c.-20-48T>G	intron_variant	5			Q5VTD9-2
GFI1B	ENST00000636137.1 linkuse as main transcript	c.-20-48T>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44090

AN:

151790

Hom.:

7680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0919

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.345

GnomAD4 exome

AF:

0.346

AC:

254436

AN:

735038

Hom.:

46610

Cov.:

AF XY:

0.339

AC XY:

130970

AN XY:

386830

show subpopulations

Gnomad4 AFR exome

AF:

0.0861

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.348

Gnomad4 EAS exome

AF:

0.279

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.371

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.290

AC:

44081

AN:

151908

Hom.:

7676

Cov.:

AF XY:

0.294

AC XY:

21794

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.0916

Gnomad4 AMR

AF:

0.392

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.343

Alfa

AF:

0.356

Hom.:

12217

Bravo

AF:

0.285

Asia WGS

AF:

0.229

AC:

795

AN:

3478

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

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.12

DANN

Benign

0.52

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