rs11568995
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001963.6(EGF):c.2053+194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,202 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.027 ( 76 hom., cov: 32)
Consequence
EGF
NM_001963.6 intron
NM_001963.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.875
Genes affected
EGF (HGNC:3229): (epidermal growth factor) This gene encodes a member of the epidermal growth factor superfamily. The encoded preproprotein is proteolytically processed to generate the 53-amino acid epidermal growth factor peptide. This protein acts a potent mitogenic factor that plays an important role in the growth, proliferation and differentiation of numerous cell types. This protein acts by binding with high affinity to the cell surface receptor, epidermal growth factor receptor. Defects in this gene are the cause of hypomagnesemia type 4. Dysregulation of this gene has been associated with the growth and progression of certain cancers. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 4-109976429-G-A is Benign according to our data. Variant chr4-109976429-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1317865.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.027 (4111/152202) while in subpopulation AFR AF= 0.045 (1869/41534). AF 95% confidence interval is 0.0433. There are 76 homozygotes in gnomad4. There are 2000 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 76 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.2053+194G>A | intron_variant | ENST00000265171.10 | |||
EGF | NM_001178130.3 | c.2053+194G>A | intron_variant | ||||
EGF | NM_001178131.3 | c.1927+194G>A | intron_variant | ||||
EGF | NM_001357021.2 | c.1927+194G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171.10 | c.2053+194G>A | intron_variant | 1 | NM_001963.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0270 AC: 4107AN: 152084Hom.: 76 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0270 AC: 4111AN: 152202Hom.: 76 Cov.: 32 AF XY: 0.0269 AC XY: 2000AN XY: 74416
GnomAD4 genome
?
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3478
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 | GeneDx | Feb 03, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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