rs221795

chr7-100685638-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375765.1(GIGYF1):c.1055-157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,110 control chromosomes in the GnomAD database, including 34,188 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34188 hom., cov: 33)
• Consequence: GIGYF1 NM_001375765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

GIGYF1 (HGNC:9126): (GRB10 interacting GYF protein 1) This gene encodes a member of the gyf family of adaptor proteins. The encoded protein contains a gyf protein interaction domain. It binds growth factor receptor bound 10, another adaptor protein that binds activated insulin-like growth factor 1 and insulin receptors and regulates receptor signaling. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIGYF1	NM_001375765.1	c.1055-157G>A		intron_variant		ENST00000678049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIGYF1	ENST00000678049.1	c.1055-157G>A		intron_variant			NM_001375765.1	P1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101494 AN: 151992 Hom.: 34173 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.727

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.668 AC: 101551 AN: 152110 Hom.: 34188 Cov.: 33 AF XY: 0.672 AC XY: 49966 AN XY: 74354

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.730

Alfa AF: 0.668 Hom.: 45327

Bravo AF: 0.680

Asia WGS AF: 0.739 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.34
Dann	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs221795; hg19: chr7-100283261;