4-109913276-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001963.6(EGF):c.-60C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,606,514 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001963.6 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171 | c.-60C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 24 | 1 | NM_001963.6 | ENSP00000265171.5 | |||
EGF | ENST00000265171 | c.-60C>T | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_001963.6 | ENSP00000265171.5 |
Frequencies
GnomAD3 genomes AF: 0.000966 AC: 147AN: 152184Hom.: 1 Cov.: 33
GnomAD4 exome AF: 0.00141 AC: 2048AN: 1454212Hom.: 0 Cov.: 30 AF XY: 0.00136 AC XY: 981AN XY: 723552
GnomAD4 genome AF: 0.000965 AC: 147AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
Renal hypomagnesemia 4 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at