rs199921300
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 2P and 14B. PM2BP4_ModerateBP6_Very_StrongBS1
The NM_025074.7(FRAS1):āc.10539A>Gā(p.Thr3513=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.00016 in 1,608,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_025074.7 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRAS1 | NM_025074.7 | c.10539A>G | p.Thr3513= | splice_region_variant, synonymous_variant | 67/74 | ENST00000512123.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRAS1 | ENST00000512123.4 | c.10539A>G | p.Thr3513= | splice_region_variant, synonymous_variant | 67/74 | 5 | NM_025074.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000874 AC: 133AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 57AN: 242420Hom.: 0 AF XY: 0.000144 AC XY: 19AN XY: 131764
GnomAD4 exome AF: 0.0000845 AC: 123AN: 1456192Hom.: 0 Cov.: 31 AF XY: 0.0000704 AC XY: 51AN XY: 724438
GnomAD4 genome ? AF: 0.000880 AC: 134AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000847 AC XY: 63AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 05, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 25, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Fraser syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 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