Variant 7-122302388-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001024613.4(FEZF1):c.1070-34del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 1,512,026 control chromosomes in the GnomAD database, including 4,265 homozygotes. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.10 ( 1635 hom., cov: 31)

Exomes 𝑓: 0.046 ( 2630 hom. )

Consequence

FEZF1
NM_001024613.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.172

Variant links:

Genes affected

FEZF1 (HGNC:22788): (FEZ family zinc finger 1) This gene encodes a transcriptional repressor that belongs to the zinc finger double domain protein family. The encoded protein is thought to play a role in the embryonic migration of gonadotropin-releasing hormone neurons into the brain. Mutations in this gene are associated with hypogonadotropic hypogonadism-22 with anosmia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

FEZF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-122302388-GA-G is Benign according to our data. Variant chr7-122302388-GA-G is described in ClinVar as [Benign]. Clinvar id is 1243725.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
FEZF1	NM_001024613.4 linkuse as main transcript	c.1070-34del	intron_variant	ENST00000442488.7	NP_001019784.2
FEZF1	NM_001160264.2 linkuse as main transcript	c.920-34del	intron_variant		NP_001153736.1
FEZF1	XM_005250337.4 linkuse as main transcript	c.1070-34del	intron_variant		XP_005250394.1
FEZF1	XM_011516202.3 linkuse as main transcript	c.920-34del	intron_variant		XP_011514504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FEZF1	ENST00000442488.7 linkuse as main transcript	c.1070-34del		intron_variant		1	NM_001024613.4	ENSP00000411145	P2	A0PJY2-1
FEZF1	ENST00000427185.2 linkuse as main transcript	c.920-34del		intron_variant		1		ENSP00000392727	A2	A0PJY2-2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15475

AN:

148442

Hom.:

1631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.0264

Gnomad AMR

AF:

0.0584

Gnomad ASJ

AF:

0.0479

Gnomad EAS

AF:

0.0115

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.148

Gnomad NFE

AF:

0.0362

Gnomad OTH

AF:

0.0927

GnomAD3 exomes

AF:

0.0864

AC:

14559

AN:

168574

Hom.:

925

AF XY:

0.0853

AC XY:

7851

AN XY:

92000

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.0612

Gnomad ASJ exome

AF:

0.0692

Gnomad EAS exome

AF:

0.0159

Gnomad SAS exome

AF:

0.156

Gnomad FIN exome

AF:

0.0222

Gnomad NFE exome

AF:

0.0567

Gnomad OTH exome

AF:

0.0801

GnomAD4 exome

AF:

0.0459

AC:

62618

AN:

1363472

Hom.:

2630

Cov.:

AF XY:

0.0478

AC XY:

32424

AN XY:

678934

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.0449

Gnomad4 ASJ exome

AF:

0.0513

Gnomad4 EAS exome

AF:

0.0204

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.0161

Gnomad4 NFE exome

AF:

0.0344

Gnomad4 OTH exome

AF:

0.0607

GnomAD4 genome

AF:

0.104

AC:

15496

AN:

148554

Hom.:

1635

Cov.:

AF XY:

0.103

AC XY:

7424

AN XY:

72378

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.0584

Gnomad4 ASJ

AF:

0.0479

Gnomad4 EAS

AF:

0.0115

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.0141

Gnomad4 NFE

AF:

0.0362

Gnomad4 OTH

AF:

0.0912

Alfa

AF:

0.0339

Hom.:

Bravo

AF:

0.113

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

Oct 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BranchPoint Hunter

1.0

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