rs372458379
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM4BS1_SupportingBS2
The NM_194277.3(FRMD7):c.2145A>T(p.Ter715Tyrext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,209,613 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194277.3 stop_lost
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.2145A>T | p.Ter715Tyrext*? | stop_lost | Exon 12 of 12 | 1 | NM_194277.3 | ENSP00000298542.3 | ||
FRMD7 | ENST00000370879.5 | c.1785A>T | p.Ter595Tyrext*? | stop_lost | Exon 8 of 8 | 1 | ENSP00000359916.1 | |||
FRMD7 | ENST00000464296.1 | c.2100A>T | p.Ter700Tyrext*? | stop_lost, splice_region_variant | Exon 12 of 12 | 1 | ENSP00000417996.1 |
Frequencies
GnomAD3 genomes AF: 0.0000800 AC: 9AN: 112467Hom.: 0 Cov.: 24 AF XY: 0.0000578 AC XY: 2AN XY: 34615
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67480
GnomAD4 exome AF: 0.00000365 AC: 4AN: 1097146Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 362566
GnomAD4 genome AF: 0.0000800 AC: 9AN: 112467Hom.: 0 Cov.: 24 AF XY: 0.0000578 AC XY: 2AN XY: 34615
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change disrupts the translational stop signal of the FRMD7 mRNA. It is expected to extend the length of the FRMD7 protein by 24 additional amino acid residues. This variant is present in population databases (rs372458379, gnomAD 0.01%). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 1008913). This variant has not been reported in the literature in individuals affected with FRMD7-related conditions. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at