9-14792753-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_001379081.2(FREM1):āc.3971T>Cā(p.Leu1324Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,596,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. L1324R) has been classified as Pathogenic.
Frequency
Consequence
NM_001379081.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.3971T>C | p.Leu1324Pro | missense_variant | Exon 22 of 37 | ENST00000380880.4 | NP_001366010.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FREM1 | ENST00000380880.4 | c.3971T>C | p.Leu1324Pro | missense_variant | Exon 22 of 37 | 5 | NM_001379081.2 | ENSP00000370262.3 | ||
FREM1 | ENST00000380875.7 | n.3971T>C | non_coding_transcript_exon_variant | Exon 23 of 31 | 1 | ENSP00000370257.3 | ||||
FREM1 | ENST00000466679.1 | n.49T>C | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 | |||||
FREM1 | ENST00000497634.2 | n.132T>C | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1444142Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 716880
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at