rs17290162
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000275493.7(EGFR):c.1788G>A(p.Pro596=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,614,122 control chromosomes in the GnomAD database, including 47 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. P596P) has been classified as Likely benign.
Frequency
Consequence
ENST00000275493.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGFR | NM_005228.5 | c.1788G>A | p.Pro596= | synonymous_variant | 15/28 | ENST00000275493.7 | NP_005219.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGFR | ENST00000275493.7 | c.1788G>A | p.Pro596= | synonymous_variant | 15/28 | 1 | NM_005228.5 | ENSP00000275493 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00814 AC: 1239AN: 152154Hom.: 19 Cov.: 33
GnomAD3 exomes AF: 0.00203 AC: 510AN: 251426Hom.: 7 AF XY: 0.00166 AC XY: 225AN XY: 135892
GnomAD4 exome AF: 0.000926 AC: 1354AN: 1461852Hom.: 28 Cov.: 31 AF XY: 0.000770 AC XY: 560AN XY: 727228
GnomAD4 genome AF: 0.00817 AC: 1244AN: 152270Hom.: 19 Cov.: 33 AF XY: 0.00817 AC XY: 608AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | May 12, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
EGFR-related lung cancer Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at