chr13-38687356-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_207361.6(FREM2):c.12C>A(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000963 in 1,453,420 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A4A) has been classified as Likely benign.
Frequency
Consequence
NM_207361.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.12C>A | p.Ala4= | synonymous_variant | 1/24 | ENST00000280481.9 | |
FREM2 | XM_017020554.2 | c.12C>A | p.Ala4= | synonymous_variant | 1/3 | ||
FREM2 | XR_941571.3 | n.280C>A | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM2 | ENST00000280481.9 | c.12C>A | p.Ala4= | synonymous_variant | 1/24 | 1 | NM_207361.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232800Hom.: 0 AF XY: 0.00000791 AC XY: 1AN XY: 126426
GnomAD4 exome AF: 0.00000963 AC: 14AN: 1453420Hom.: 0 Cov.: 30 AF XY: 0.00000831 AC XY: 6AN XY: 722250
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at