rs374074686
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018027.5(FRMD4A):c.2879G>T(p.Ser960Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000189 in 1,584,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. S960N) has been classified as Uncertain significance.
Frequency
Consequence
NM_018027.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMD4A | NM_018027.5 | c.2879G>T | p.Ser960Ile | missense_variant | Exon 22 of 25 | ENST00000357447.7 | NP_060497.3 | |
FRMD4A | NM_001318337.2 | c.2978G>T | p.Ser993Ile | missense_variant | Exon 21 of 24 | NP_001305266.1 | ||
FRMD4A | NM_001318336.2 | c.2927G>T | p.Ser976Ile | missense_variant | Exon 21 of 24 | NP_001305265.1 | ||
FRMD4A | NM_001318338.2 | c.1952G>T | p.Ser651Ile | missense_variant | Exon 11 of 14 | NP_001305267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMD4A | ENST00000357447.7 | c.2879G>T | p.Ser960Ile | missense_variant | Exon 22 of 25 | 1 | NM_018027.5 | ENSP00000350032.2 | ||
FRMD4A | ENST00000495956.3 | c.2879G>T | p.Ser960Ile | missense_variant | Exon 22 of 24 | 2 | ENSP00000488764.2 | |||
PRPF18 | ENST00000593351.2 | n.47+8480C>A | intron_variant | Intron 1 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1432472Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 712252
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at