rs776773158
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013280.5(FLRT1):c.776C>A(p.Ser259Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000688 in 1,454,354 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. Synonymous variant affecting the same amino acid position (i.e. S259S) has been classified as Likely benign.
Frequency
Consequence
NM_013280.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLRT1 | NM_013280.5 | c.776C>A | p.Ser259Ter | stop_gained | 3/3 | ENST00000682287.1 | |
MACROD1 | NM_014067.4 | c.517+34196G>T | intron_variant | ENST00000255681.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT1 | ENST00000682287.1 | c.776C>A | p.Ser259Ter | stop_gained | 3/3 | NM_013280.5 | P1 | ||
MACROD1 | ENST00000255681.7 | c.517+34196G>T | intron_variant | 1 | NM_014067.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232298Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126136
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1454354Hom.: 0 Cov.: 88 AF XY: 0.00000138 AC XY: 1AN XY: 723066
GnomAD4 genome ? Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at