chr4-78482528-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_025074.7(FRAS1):c.8745C>T(p.Phe2915Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,612,948 control chromosomes in the GnomAD database, including 37,424 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_025074.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRAS1 | ENST00000512123.4 | c.8745C>T | p.Phe2915Phe | synonymous_variant | Exon 58 of 74 | 5 | NM_025074.7 | ENSP00000422834.2 | ||
FRAS1 | ENST00000682513.1 | c.8745C>T | p.Phe2915Phe | synonymous_variant | Exon 58 of 64 | ENSP00000508201.1 |
Frequencies
GnomAD3 genomes AF: 0.220 AC: 33423AN: 152012Hom.: 4204 Cov.: 33
GnomAD3 exomes AF: 0.163 AC: 40480AN: 248552Hom.: 4274 AF XY: 0.159 AC XY: 21422AN XY: 134798
GnomAD4 exome AF: 0.203 AC: 296670AN: 1460818Hom.: 33217 Cov.: 34 AF XY: 0.198 AC XY: 143856AN XY: 726656
GnomAD4 genome AF: 0.220 AC: 33457AN: 152130Hom.: 4207 Cov.: 33 AF XY: 0.212 AC XY: 15761AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Fraser syndrome 1 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at