rs745846839
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_194277.3(FRMD7):c.2067_2069delAGA(p.Glu689del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000661 in 1,209,675 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194277.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMD7 | ENST00000298542.9 | c.2067_2069delAGA | p.Glu689del | disruptive_inframe_deletion | Exon 12 of 12 | 1 | NM_194277.3 | ENSP00000298542.3 | ||
FRMD7 | ENST00000464296.1 | c.2022_2024delAGA | p.Glu674del | disruptive_inframe_deletion | Exon 12 of 12 | 1 | ENSP00000417996.1 | |||
FRMD7 | ENST00000370879.5 | c.1707_1709delAGA | p.Glu569del | disruptive_inframe_deletion | Exon 8 of 8 | 1 | ENSP00000359916.1 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 111954Hom.: 0 Cov.: 23 AF XY: 0.0000587 AC XY: 2AN XY: 34098
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182785Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67485
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1097721Hom.: 0 AF XY: 0.00000551 AC XY: 2AN XY: 363159
GnomAD4 genome AF: 0.0000268 AC: 3AN: 111954Hom.: 0 Cov.: 23 AF XY: 0.0000587 AC XY: 2AN XY: 34098
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.2067_2069del, results in the deletion of 1 amino acid(s) of the FRMD7 protein (p.Glu689del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs745846839, gnomAD 0.008%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with FRMD7-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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