rs41321844
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005228.5(EGFR):c.3485G>A(p.Ser1162Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00064 in 1,614,152 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1162R) has been classified as Uncertain significance.
Frequency
Consequence
NM_005228.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGFR | NM_005228.5 | c.3485G>A | p.Ser1162Asn | missense_variant | 28/28 | ENST00000275493.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGFR | ENST00000275493.7 | c.3485G>A | p.Ser1162Asn | missense_variant | 28/28 | 1 | NM_005228.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00342 AC: 520AN: 152150Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.000877 AC: 220AN: 250970Hom.: 2 AF XY: 0.000649 AC XY: 88AN XY: 135640
GnomAD4 exome AF: 0.000353 AC: 516AN: 1461884Hom.: 2 Cov.: 31 AF XY: 0.000294 AC XY: 214AN XY: 727240
GnomAD4 genome AF: 0.00340 AC: 517AN: 152268Hom.: 4 Cov.: 32 AF XY: 0.00348 AC XY: 259AN XY: 74458
ClinVar
Submissions by phenotype
Lung cancer;C4015130:Inflammatory skin and bowel disease, neonatal, 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 14, 2022 | - - |
EGFR-related lung cancer Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at