chr13-38690553-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207361.6(FREM2):āc.3209T>Cā(p.Phe1070Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,613,692 control chromosomes in the GnomAD database, including 84,064 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_207361.6 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 |
---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.3209T>C | p.Phe1070Ser | missense_variant | 1/24 | ENST00000280481.9 | |
FREM2 | XM_017020554.2 | c.3209T>C | p.Phe1070Ser | missense_variant | 1/3 | ||
FREM2 | XR_941571.3 | n.3477T>C | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM2 | ENST00000280481.9 | c.3209T>C | p.Phe1070Ser | missense_variant | 1/24 | 1 | NM_207361.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.426 AC: 64680AN: 152008Hom.: 17039 Cov.: 33
GnomAD3 exomes AF: 0.342 AC: 85988AN: 251426Hom.: 16757 AF XY: 0.326 AC XY: 44307AN XY: 135886
GnomAD4 exome AF: 0.291 AC: 424958AN: 1461566Hom.: 66968 Cov.: 40 AF XY: 0.288 AC XY: 209697AN XY: 727080
GnomAD4 genome AF: 0.426 AC: 64795AN: 152126Hom.: 17096 Cov.: 33 AF XY: 0.425 AC XY: 31634AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 09, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 03, 2021 | - - |
Fraser syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 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. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | This variant is associated with the following publications: (PMID: 17000706) - |
Isolated cryptophthalmia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Fraser syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at