9-14737408-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001379081.2(FREM1):c.6528C>T(p.Ser2176Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000435 in 1,613,320 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001379081.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.6528C>T | p.Ser2176Ser | synonymous_variant | Exon 37 of 37 | ENST00000380880.4 | NP_001366010.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00225 AC: 342AN: 152060Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000563 AC: 140AN: 248756Hom.: 0 AF XY: 0.000430 AC XY: 58AN XY: 134976
GnomAD4 exome AF: 0.000235 AC: 343AN: 1461142Hom.: 1 Cov.: 29 AF XY: 0.000208 AC XY: 151AN XY: 726836
GnomAD4 genome AF: 0.00235 AC: 358AN: 152178Hom.: 5 Cov.: 32 AF XY: 0.00223 AC XY: 166AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
- -
Oculotrichoanal syndrome 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 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