chr13-38687428-C-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_207361.6(FREM2):c.84C>G(p.Pro28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,601,794 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P28P) has been classified as Likely benign.
Frequency
Consequence
NM_207361.6 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 |
---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.84C>G | p.Pro28= | synonymous_variant | 1/24 | ENST00000280481.9 | |
FREM2 | XM_017020554.2 | c.84C>G | p.Pro28= | synonymous_variant | 1/3 | ||
FREM2 | XR_941571.3 | n.352C>G | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM2 | ENST00000280481.9 | c.84C>G | p.Pro28= | synonymous_variant | 1/24 | 1 | NM_207361.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00330 AC: 502AN: 152256Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00194 AC: 432AN: 222424Hom.: 3 AF XY: 0.00186 AC XY: 226AN XY: 121238
GnomAD4 exome AF: 0.00121 AC: 1760AN: 1449420Hom.: 7 Cov.: 30 AF XY: 0.00125 AC XY: 899AN XY: 720028
GnomAD4 genome ? AF: 0.00329 AC: 502AN: 152374Hom.: 1 Cov.: 34 AF XY: 0.00342 AC XY: 255AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | FREM2: BP4, BP7 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 12, 2014 | - - |
Isolated cryptophthalmia;C4540036:Fraser syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 13, 2021 | - - |
Fraser syndrome 2 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