rs199624326
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001375765.1(GIGYF1):c.1192+14A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00343 in 1,584,222 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0035 ( 10 hom. )
Consequence
GIGYF1
NM_001375765.1 intron
NM_001375765.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.27
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 7-100685330-T-A is Benign according to our data. Variant chr7-100685330-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 445298.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIGYF1 | NM_001375765.1 | c.1192+14A>T | intron_variant | ENST00000678049.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIGYF1 | ENST00000678049.1 | c.1192+14A>T | intron_variant | NM_001375765.1 | P1 | ||||
GIGYF1 | ENST00000275732.5 | c.1192+14A>T | intron_variant | 1 | P1 | ||||
GIGYF1 | ENST00000646601.1 | c.1192+14A>T | intron_variant | P1 | |||||
GIGYF1 | ENST00000471340.2 | n.422-436A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00312 AC: 474AN: 152154Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00362 AC: 822AN: 226902Hom.: 2 AF XY: 0.00357 AC XY: 441AN XY: 123424
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GnomAD4 exome AF: 0.00347 AC: 4964AN: 1431950Hom.: 10 Cov.: 33 AF XY: 0.00338 AC XY: 2407AN XY: 711372
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GnomAD4 genome ? AF: 0.00311 AC: 474AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00363 AC XY: 270AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 20, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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