rs11569098
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001963.6(EGF):c.3127C>T(p.Leu1043Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,613,918 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001963.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.3127C>T | p.Leu1043Phe | missense_variant | 21/24 | ENST00000265171.10 | |
EGF | NM_001178130.3 | c.3004C>T | p.Leu1002Phe | missense_variant | 20/23 | ||
EGF | NM_001178131.3 | c.3001C>T | p.Leu1001Phe | missense_variant | 20/23 | ||
EGF | NM_001357021.2 | c.2758C>T | p.Leu920Phe | missense_variant | 18/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171.10 | c.3127C>T | p.Leu1043Phe | missense_variant | 21/24 | 1 | NM_001963.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00837 AC: 1274AN: 152140Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.00224 AC: 562AN: 251446Hom.: 10 AF XY: 0.00140 AC XY: 190AN XY: 135898
GnomAD4 exome AF: 0.000850 AC: 1242AN: 1461660Hom.: 15 Cov.: 32 AF XY: 0.000700 AC XY: 509AN XY: 727140
GnomAD4 genome AF: 0.00838 AC: 1276AN: 152258Hom.: 22 Cov.: 32 AF XY: 0.00828 AC XY: 616AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at