chr10-13656906-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018027.5(FRMD4A):c.2683C>T(p.Arg895Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,486,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R895H) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD4A | NM_018027.5 | c.2683C>T | p.Arg895Cys | missense_variant | 22/25 | ENST00000357447.7 | |
FRMD4A | NM_001318337.2 | c.2782C>T | p.Arg928Cys | missense_variant | 21/24 | ||
FRMD4A | NM_001318336.2 | c.2731C>T | p.Arg911Cys | missense_variant | 21/24 | ||
FRMD4A | NM_001318338.2 | c.1756C>T | p.Arg586Cys | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD4A | ENST00000357447.7 | c.2683C>T | p.Arg895Cys | missense_variant | 22/25 | 1 | NM_018027.5 | P2 | |
FRMD4A | ENST00000495956.3 | c.2683C>T | p.Arg895Cys | missense_variant | 22/24 | 2 | A2 | ||
PRPF18 | ENST00000593351.2 | n.47+8676G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000727 AC: 11AN: 151314Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 14AN: 113744Hom.: 0 AF XY: 0.000123 AC XY: 8AN XY: 65238
GnomAD4 exome AF: 0.000124 AC: 166AN: 1335434Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 80AN XY: 659840
GnomAD4 genome AF: 0.0000727 AC: 11AN: 151314Hom.: 0 Cov.: 32 AF XY: 0.0000947 AC XY: 7AN XY: 73936
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.2683C>T (p.R895C) alteration is located in exon 22 (coding exon 21) of the FRMD4A gene. This alteration results from a C to T substitution at nucleotide position 2683, causing the arginine (R) at amino acid position 895 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at