chr7-55191757-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005228.5(EGFR):c.2508C>T(p.Arg836=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 1,613,938 control chromosomes in the GnomAD database, including 479 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R836R) has been classified as Likely benign.
Frequency
Consequence
NM_005228.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGFR | NM_005228.5 | c.2508C>T | p.Arg836= | synonymous_variant | 21/28 | ENST00000275493.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGFR | ENST00000275493.7 | c.2508C>T | p.Arg836= | synonymous_variant | 21/28 | 1 | NM_005228.5 | P1 | |
EGFR | ENST00000455089.5 | c.2373C>T | p.Arg791= | synonymous_variant | 20/26 | 1 | |||
EGFR | ENST00000450046.2 | c.2349C>T | p.Arg783= | synonymous_variant | 21/28 | 4 | |||
EGFR | ENST00000700145.1 | c.858C>T | p.Arg286= | synonymous_variant | 8/9 |
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2441AN: 152016Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.0165 AC: 4153AN: 251218Hom.: 67 AF XY: 0.0166 AC XY: 2255AN XY: 135764
GnomAD4 exome AF: 0.0219 AC: 31945AN: 1461804Hom.: 446 Cov.: 31 AF XY: 0.0212 AC XY: 15445AN XY: 727208
GnomAD4 genome AF: 0.0160 AC: 2440AN: 152134Hom.: 33 Cov.: 32 AF XY: 0.0160 AC XY: 1190AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 24, 2007 | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | May 28, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2021 | This variant is associated with the following publications: (PMID: 24899223, 22192147) - |
EGFR-related lung cancer Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Lung cancer Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at