7-100681753-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001375765.1(GIGYF1):c.3074C>T(p.Ser1025Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00022 in 1,584,510 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 0.00015 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
GIGYF1
NM_001375765.1 missense
NM_001375765.1 missense
Scores
9
9
Clinical Significance
Conservation
PhyloP100: 5.93
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 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12665).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIGYF1 | NM_001375765.1 | c.3074C>T | p.Ser1025Phe | missense_variant | 27/27 | ENST00000678049.1 | NP_001362694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIGYF1 | ENST00000678049.1 | c.3074C>T | p.Ser1025Phe | missense_variant | 27/27 | NM_001375765.1 | ENSP00000503354.1 | |||
GIGYF1 | ENST00000275732.5 | c.3074C>T | p.Ser1025Phe | missense_variant | 24/24 | 1 | ENSP00000275732.4 | |||
GIGYF1 | ENST00000646601.1 | c.3074C>T | p.Ser1025Phe | missense_variant | 28/28 | ENSP00000494292.1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152242Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000261 AC: 59AN: 226364Hom.: 0 AF XY: 0.000231 AC XY: 28AN XY: 121418
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GnomAD4 exome AF: 0.000228 AC: 326AN: 1432268Hom.: 0 Cov.: 32 AF XY: 0.000211 AC XY: 150AN XY: 709250
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74382
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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 06, 2021 | The c.3074C>T (p.S1025F) alteration is located in exon 24 (coding exon 24) of the GIGYF1 gene. This alteration results from a C to T substitution at nucleotide position 3074, causing the serine (S) at amino acid position 1025 to be replaced by a phenylalanine (F). 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
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.
REVEL
Uncertain
Sift
Uncertain
D;.
Sift4G
Uncertain
D;.
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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