chr7-100681721-A-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM4PP5_Moderate

The NM_001375765.1(GIGYF1):​c.3106T>G​(p.Ter1036GlyextTer72) variant causes a stop lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 33)

Consequence

GIGYF1
NM_001375765.1 stop_lost

Scores

2
1
4

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 4.02
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Stoplost variant in NM_001375765.1 Downstream stopcodon found after 27 codons.
PP5
Variant 7-100681721-A-C is Pathogenic according to our data. Variant chr7-100681721-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 2430005.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GIGYF1NM_001375765.1 linkuse as main transcriptc.3106T>G p.Ter1036GlyextTer72 stop_lost 27/27 ENST00000678049.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GIGYF1ENST00000678049.1 linkuse as main transcriptc.3106T>G p.Ter1036GlyextTer72 stop_lost 27/27 NM_001375765.1 P1
GIGYF1ENST00000275732.5 linkuse as main transcriptc.3106T>G p.Ter1036GlyextTer72 stop_lost 24/241 P1
GIGYF1ENST00000646601.1 linkuse as main transcriptc.3106T>G p.Ter1036GlyextTer72 stop_lost 28/28 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Autism spectrum disorder Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingDepartment of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
14
DANN
Benign
0.92
Eigen
Pathogenic
1.0
Eigen_PC
Pathogenic
0.87
FATHMM_MKL
Uncertain
0.97
D
MutationTaster
Benign
1.0
N
Vest4
0.094
GERP RS
5.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-100279344; API