4-109912889-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001963.6(EGF):c.-447G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000776 in 179,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001963.6 5_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.-447G>A | 5_prime_UTR_variant | Exon 1 of 24 | ENST00000265171.10 | NP_001954.2 | ||
EGF | NM_001178130.3 | c.-447G>A | 5_prime_UTR_variant | Exon 1 of 23 | NP_001171601.1 | |||
EGF | NM_001178131.3 | c.-447G>A | 5_prime_UTR_variant | Exon 1 of 23 | NP_001171602.1 | |||
EGF | NM_001357021.2 | c.-447G>A | 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.-447G>A | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_001963.6 | ENSP00000265171.5 | |||
EGF | ENST00000509793 | c.-447G>A | 5_prime_UTR_variant | Exon 1 of 23 | 2 | ENSP00000424316.1 | ||||
EGF | ENST00000652245 | c.-447G>A | 5_prime_UTR_variant | Exon 1 of 20 | ENSP00000498337.1 |
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152202Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000560 AC: 15AN: 26766Hom.: 0 Cov.: 0 AF XY: 0.000444 AC XY: 6AN XY: 13510
GnomAD4 genome AF: 0.000814 AC: 124AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000846 AC XY: 63AN XY: 74482
ClinVar
Submissions by phenotype
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at