7-100682382-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001375765.1(GIGYF1):c.2701G>A(p.Gly901Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000533 in 1,613,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
GIGYF1
NM_001375765.1 missense
NM_001375765.1 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 6.15
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37689555).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIGYF1 | NM_001375765.1 | c.2701G>A | p.Gly901Ser | missense_variant | 24/27 | ENST00000678049.1 | NP_001362694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIGYF1 | ENST00000678049.1 | c.2701G>A | p.Gly901Ser | missense_variant | 24/27 | NM_001375765.1 | ENSP00000503354.1 | |||
GIGYF1 | ENST00000275732.5 | c.2701G>A | p.Gly901Ser | missense_variant | 21/24 | 1 | ENSP00000275732.4 | |||
GIGYF1 | ENST00000646601.1 | c.2701G>A | p.Gly901Ser | missense_variant | 25/28 | ENSP00000494292.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000608 AC: 15AN: 246838Hom.: 0 AF XY: 0.0000674 AC XY: 9AN XY: 133488
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GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461340Hom.: 0 Cov.: 33 AF XY: 0.0000523 AC XY: 38AN XY: 726982
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74500
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.2701G>A (p.G901S) alteration is located in exon 21 (coding exon 21) of the GIGYF1 gene. This alteration results from a G to A substitution at nucleotide position 2701, causing the glycine (G) at amino acid position 901 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.
REVEL
Uncertain
Sift
Benign
T;.
Sift4G
Benign
T;.
Polyphen
D;D
Vest4
MutPred
Gain of disorder (P = 0.0961);Gain of disorder (P = 0.0961);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at