7-100682365-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001375765.1(GIGYF1):c.2718C>T(p.Cys906Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,613,464 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 3 hom. )
Consequence
GIGYF1
NM_001375765.1 synonymous
NM_001375765.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0850
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_benign. Variant got -5 ACMG points.
BP6
Variant 7-100682365-G-A is Benign according to our data. Variant chr7-100682365-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3038257.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIGYF1 | NM_001375765.1 | c.2718C>T | p.Cys906Cys | synonymous_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.2718C>T | p.Cys906Cys | synonymous_variant | 24/27 | NM_001375765.1 | ENSP00000503354.1 | |||
GIGYF1 | ENST00000275732.5 | c.2718C>T | p.Cys906Cys | synonymous_variant | 21/24 | 1 | ENSP00000275732.4 | |||
GIGYF1 | ENST00000646601.1 | c.2718C>T | p.Cys906Cys | synonymous_variant | 25/28 | ENSP00000494292.1 |
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 281AN: 152214Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00148 AC: 365AN: 246496Hom.: 1 AF XY: 0.00148 AC XY: 198AN XY: 133380
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GnomAD4 exome AF: 0.00222 AC: 3242AN: 1461132Hom.: 3 Cov.: 33 AF XY: 0.00215 AC XY: 1563AN XY: 726884
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GnomAD4 genome AF: 0.00184 AC: 281AN: 152332Hom.: 1 Cov.: 33 AF XY: 0.00179 AC XY: 133AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GIGYF1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
DS_DG_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at