5-38338764-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152403.4(EGFLAM):c.274C>T(p.Arg92Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152403.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGFLAM | NM_152403.4 | c.274C>T | p.Arg92Trp | missense_variant | 3/22 | ENST00000322350.10 | NP_689616.2 | |
EGFLAM | NM_001205301.2 | c.274C>T | p.Arg92Trp | missense_variant | 3/23 | NP_001192230.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGFLAM | ENST00000322350.10 | c.274C>T | p.Arg92Trp | missense_variant | 3/22 | 1 | NM_152403.4 | ENSP00000313084 | P3 | |
EGFLAM | ENST00000354891.7 | c.274C>T | p.Arg92Trp | missense_variant | 3/23 | 1 | ENSP00000346964 | A2 | ||
EGFLAM | ENST00000504709.1 | c.*316C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 3 | ENSP00000426437 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251346Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135848
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461858Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.274C>T (p.R92W) alteration is located in exon 3 (coding exon 3) of the EGFLAM gene. This alteration results from a C to T substitution at nucleotide position 274, causing the arginine (R) at amino acid position 92 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at