Genetic Variant GIGYF2:c.268-6delT (chr2-232756197-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001103146.3(GIGYF2):c.268-6delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.086 ( 407 hom., cov: 0)

Exomes 𝑓: 0.12 ( 6 hom. )

Consequence

GIGYF2
NM_001103146.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.876

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIGYF2	NM_001103146.3 link	c.268-6delT		splice_region_variant, intron_variant	Intron 5 of 28	ENST00000373563.9	NP_001096616.1	Q6Y7W6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIGYF2	ENST00000373563.9 link	c.268-25delT		intron_variant	Intron 5 of 28	1	NM_001103146.3	ENSP00000362664.5		Q6Y7W6-1

Frequencies

GnomAD3 genomes

AF:

0.0864

AC:

8860

AN:

102604

Hom.:

408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.00137

Gnomad AMR

AF:

0.0834

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.0640

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.0291

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.0693

GnomAD4 exome

AF:

0.121

AC:

71627

AN:

592778

Hom.:

Cov.:

AF XY:

0.117

AC XY:

36883

AN XY:

313970

show subpopulations

Gnomad4 AFR exome

AF:

0.211

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.113

Gnomad4 EAS exome

AF:

0.202

Gnomad4 SAS exome

AF:

0.0877

Gnomad4 FIN exome

AF:

0.125

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.0864

AC:

8861

AN:

102572

Hom.:

407

Cov.:

AF XY:

0.0904

AC XY:

4297

AN XY:

47530

show subpopulations

Gnomad4 AFR

AF:

0.247

Gnomad4 AMR

AF:

0.0837

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.0642

Gnomad4 FIN

AF:

0.0237

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.0686

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over