Variant rs10555297 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001103146.3(GIGYF2):c.3630_3632del(p.Gln1216del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.574 in 1,526,600 control chromosomes in the GnomAD database, including 244,405 homozygotes. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P1210P) has been classified as Benign.

Frequency

Genomes: 𝑓 0.61 ( 25547 hom., cov: 0)

Exomes 𝑓: 0.57 ( 218858 hom. )

Consequence

GIGYF2
NM_001103146.3 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 4.44

Variant links:

Genes affected

GIGYF2 (HGNC:11960): (GRB10 interacting GYF protein 2) This gene contains CAG trinucleotide repeats and encodes a protein containing several stretches of polyglutamine residues. The encoded protein may be involved in the regulation of tyrosine kinase receptor signaling. This gene is located in a chromosomal region that was genetically linked to Parkinson disease type 11, and mutations in this gene were thought to be causative for this disease. However, more recent studies in different populations have been unable to replicate this association. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

GIGYF2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-232847516-CACA-C is Benign according to our data. Variant chr2-232847516-CACA-C is described in ClinVar as [Benign]. Clinvar id is 518338.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-232847516-CACA-C is described in Lovd as [Likely_benign]. Variant chr2-232847516-CACA-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIGYF2	NM_001103146.3 linkuse as main transcript	c.3630_3632del	p.Gln1216del	inframe_deletion	27/29	ENST00000373563.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIGYF2	ENST00000373563.9 linkuse as main transcript	c.3630_3632del	p.Gln1216del	inframe_deletion	27/29	1	NM_001103146.3	P4	Q6Y7W6-1

Frequencies

GnomAD3 genomes

AF:

0.612

AC:

87265

AN:

142576

Hom.:

25523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.647

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.702

Gnomad MID

AF:

0.550

Gnomad NFE

AF:

0.611

Gnomad OTH

AF:

0.628

GnomAD3 exomes

AF:

0.557

AC:

129291

AN:

232056

Hom.:

37165

AF XY:

0.541

AC XY:

68565

AN XY:

126696

show subpopulations

Gnomad AFR exome

AF:

0.597

Gnomad AMR exome

AF:

0.654

Gnomad ASJ exome

AF:

0.612

Gnomad EAS exome

AF:

0.505

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.694

Gnomad NFE exome

AF:

0.576

Gnomad OTH exome

AF:

0.552

GnomAD4 exome

AF:

0.570

AC:

789195

AN:

1383896

Hom.:

218858

AF XY:

0.562

AC XY:

386735

AN XY:

688594

show subpopulations

Gnomad4 AFR exome

AF:

0.608

Gnomad4 AMR exome

AF:

0.644

Gnomad4 ASJ exome

AF:

0.627

Gnomad4 EAS exome

AF:

0.456

Gnomad4 SAS exome

AF:

0.272

Gnomad4 FIN exome

AF:

0.672

Gnomad4 NFE exome

AF:

0.588

Gnomad4 OTH exome

AF:

0.561

GnomAD4 genome

AF:

0.612

AC:

87347

AN:

142704

Hom.:

25547

Cov.:

AF XY:

0.613

AC XY:

42699

AN XY:

69682

show subpopulations

Gnomad4 AFR

AF:

0.615

Gnomad4 AMR

AF:

0.647

Gnomad4 ASJ

AF:

0.642

Gnomad4 EAS

AF:

0.537

Gnomad4 SAS

AF:

0.311

Gnomad4 FIN

AF:

0.702

Gnomad4 NFE

AF:

0.611

Gnomad4 OTH

AF:

0.621

Alfa

AF:

0.545

Hom.:

1638

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Parkinson disease 11, autosomal dominant, susceptibility to

Benign:1

Benign, no assertion criteria provided

clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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