X-132077924-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_194277.3(FRMD7):c.2093C>A(p.Pro698Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,096,615 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMD7 | ENST00000298542.9 | c.2093C>A | p.Pro698Gln | missense_variant | Exon 12 of 12 | 1 | NM_194277.3 | ENSP00000298542.3 | ||
FRMD7 | ENST00000464296.1 | c.2048C>A | p.Pro683Gln | missense_variant | Exon 12 of 12 | 1 | ENSP00000417996.1 | |||
FRMD7 | ENST00000370879.5 | c.1733C>A | p.Pro578Gln | missense_variant | Exon 8 of 8 | 1 | ENSP00000359916.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182789Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67495
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1096615Hom.: 0 Cov.: 30 AF XY: 0.00000829 AC XY: 3AN XY: 362029
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 698 of the FRMD7 protein (p.Pro698Gln). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with FRMD7-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at