chr4-109913381-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001963.6(EGF):āc.46A>Cā(p.Ser16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,613,952 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S16T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001963.6 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGF | NM_001963.6 | c.46A>C | p.Ser16Arg | missense_variant | 1/24 | ENST00000265171.10 | |
EGF | NM_001178130.3 | c.46A>C | p.Ser16Arg | missense_variant | 1/23 | ||
EGF | NM_001178131.3 | c.46A>C | p.Ser16Arg | missense_variant | 1/23 | ||
EGF | NM_001357021.2 | c.46A>C | p.Ser16Arg | missense_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGF | ENST00000265171.10 | c.46A>C | p.Ser16Arg | missense_variant | 1/24 | 1 | NM_001963.6 | P1 | |
EGF | ENST00000503392.1 | c.46A>C | p.Ser16Arg | missense_variant | 1/23 | 1 | |||
EGF | ENST00000509793.5 | c.46A>C | p.Ser16Arg | missense_variant | 1/23 | 2 | |||
EGF | ENST00000652245.1 | c.46A>C | p.Ser16Arg | missense_variant | 1/20 |
Frequencies
GnomAD3 genomes AF: 0.00323 AC: 491AN: 152144Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00450 AC: 1131AN: 251146Hom.: 16 AF XY: 0.00430 AC XY: 584AN XY: 135754
GnomAD4 exome AF: 0.00178 AC: 2606AN: 1461690Hom.: 33 Cov.: 31 AF XY: 0.00169 AC XY: 1226AN XY: 727150
GnomAD4 genome AF: 0.00323 AC: 492AN: 152262Hom.: 7 Cov.: 32 AF XY: 0.00451 AC XY: 336AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 20, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | See Variant Classification Assertion Criteria. - |
Renal hypomagnesemia 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at