chr4-78499857-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_025074.7(FRAS1):c.9252G>T(p.Arg3084=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,613,000 control chromosomes in the GnomAD database, including 31,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R3084R) has been classified as Likely benign.
Frequency
Consequence
NM_025074.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRAS1 | NM_025074.7 | c.9252G>T | p.Arg3084= | synonymous_variant | 61/74 | ENST00000512123.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRAS1 | ENST00000512123.4 | c.9252G>T | p.Arg3084= | synonymous_variant | 61/74 | 5 | NM_025074.7 | P1 | |
FRAS1 | ENST00000682513.1 | c.9252G>T | p.Arg3084= | synonymous_variant | 61/64 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21945AN: 152092Hom.: 1897 Cov.: 32
GnomAD3 exomes AF: 0.140 AC: 34863AN: 248832Hom.: 3240 AF XY: 0.140 AC XY: 18917AN XY: 134982
GnomAD4 exome AF: 0.191 AC: 279029AN: 1460790Hom.: 29726 Cov.: 34 AF XY: 0.187 AC XY: 135687AN XY: 726624
GnomAD4 genome AF: 0.144 AC: 21945AN: 152210Hom.: 1897 Cov.: 32 AF XY: 0.138 AC XY: 10305AN XY: 74426
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Fraser syndrome 1 Benign:1
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 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