4-109912954-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001963.6(EGF):c.-382A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 241,254 control chromosomes in the GnomAD database, including 29,908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001963.6 5_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 24 | ENST00000265171.10 | NP_001954.2 | ||
EGF | NM_001178130.3 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 23 | NP_001171601.1 | |||
EGF | NM_001178131.3 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 23 | NP_001171602.1 | |||
EGF | NM_001357021.2 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 20 | NP_001343950.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_001963.6 | ENSP00000265171.5 | |||
EGF | ENST00000509793 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 23 | 2 | ENSP00000424316.1 | ||||
EGF | ENST00000652245 | c.-382A>G | 5_prime_UTR_variant | Exon 1 of 20 | ENSP00000498337.1 |
Frequencies
GnomAD3 genomes AF: 0.506 AC: 76812AN: 151930Hom.: 20905 Cov.: 33
GnomAD4 exome AF: 0.433 AC: 38620AN: 89206Hom.: 8960 Cov.: 0 AF XY: 0.440 AC XY: 20451AN XY: 46492
GnomAD4 genome AF: 0.506 AC: 76910AN: 152048Hom.: 20948 Cov.: 33 AF XY: 0.505 AC XY: 37518AN XY: 74308
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 17851837, 19179548, 14973082, 19520791, 17175377, 22236006, 17433039, 21440548, 23403233, 22782629, 22106858, 22621366, 18167406, 20203692, 22129558, 19840254, 22829952, 11844511) -
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Renal hypomagnesemia 4 Benign: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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Cholangiocarcinoma Other:1
No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at