4-109913382-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001963.6(EGF):c.47G>C(p.Ser16Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,613,854 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001963.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 24 | ENST00000265171.10 | NP_001954.2 | |
EGF | NM_001178130.3 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 23 | NP_001171601.1 | ||
EGF | NM_001178131.3 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 23 | NP_001171602.1 | ||
EGF | NM_001357021.2 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 20 | NP_001343950.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171.10 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 24 | 1 | NM_001963.6 | ENSP00000265171.5 | ||
EGF | ENST00000503392.1 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 23 | 1 | ENSP00000421384.1 | |||
EGF | ENST00000509793.5 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 23 | 2 | ENSP00000424316.1 | |||
EGF | ENST00000652245.1 | c.47G>C | p.Ser16Thr | missense_variant | Exon 1 of 20 | ENSP00000498337.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000275 AC: 69AN: 251130Hom.: 1 AF XY: 0.000309 AC XY: 42AN XY: 135750
GnomAD4 exome AF: 0.000244 AC: 356AN: 1461700Hom.: 1 Cov.: 31 AF XY: 0.000260 AC XY: 189AN XY: 727156
GnomAD4 genome AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:2
BP4 -
This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 16 of the EGF protein (p.Ser16Thr). This variant is present in population databases (rs200394315, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with EGF-related conditions. ClinVar contains an entry for this variant (Variation ID: 347225). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Hereditary renal cell carcinoma Uncertain:1
The pSer16Thr variant (rs200394315) was found at heterozygosity in an individual affected by renal cancer, her non-affected sister and their father. In InterVar, the variant is classified as PP2 (supporting pathogenic) for missense in a gene that has a low rate in benign missense variation, and in which missense variants are a common mechanism of disease. In the GnomAD database (Lek et al. 2016), this variant is overrepresented in the Ashkenazi Jewish population with an allele count of 15/10146 versus 69/276870 in the total population. Other variations of residue include Ser16Arg (1303/276890 with over-representation in East Asian and European Finnish) and Ser16Asn (1 case). Based on Signal 4.0, NCBI describes the pre-protein (reference sequence NP_001954.2) as comprising a signal peptide (SP) at amino acids 1-14. In contrast, UniProt for reference sequence P0113 indicates a cleavage of a signal sequence after amino acid 22. For both predictions, an amino acid change at residue 16 plausibly affects insertion of the pro-EGF precursor into the ER, and hence levels of secretion. No evidence of pathogenicity is reported so this variant is interpreted as VUS. -
Renal hypomagnesemia 4 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at