13-38687525-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207361.6(FREM2):c.181G>A(p.Ala61Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000375 in 1,598,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A61P) has been classified as Uncertain significance.
Frequency
Consequence
NM_207361.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.181G>A | p.Ala61Thr | missense_variant | 1/24 | ENST00000280481.9 | |
FREM2 | XM_017020554.2 | c.181G>A | p.Ala61Thr | missense_variant | 1/3 | ||
FREM2 | XR_941571.3 | n.449G>A | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM2 | ENST00000280481.9 | c.181G>A | p.Ala61Thr | missense_variant | 1/24 | 1 | NM_207361.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152250Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1446344Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 717728
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152250Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at