rs760597864
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001368397.1(FRMPD4):c.2048A>G(p.Glu683Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000156 in 1,207,431 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 60 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001368397.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMPD4 | NM_001368397.1 | c.2048A>G | p.Glu683Gly | missense_variant | 15/17 | ENST00000675598.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMPD4 | ENST00000675598.1 | c.2048A>G | p.Glu683Gly | missense_variant | 15/17 | NM_001368397.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000361 AC: 4AN: 110721Hom.: 0 Cov.: 22 AF XY: 0.0000304 AC XY: 1AN XY: 32939
GnomAD3 exomes AF: 0.0000491 AC: 9AN: 183361Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67799
GnomAD4 exome AF: 0.000168 AC: 184AN: 1096710Hom.: 0 Cov.: 32 AF XY: 0.000163 AC XY: 59AN XY: 362106
GnomAD4 genome ? AF: 0.0000361 AC: 4AN: 110721Hom.: 0 Cov.: 22 AF XY: 0.0000304 AC XY: 1AN XY: 32939
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 28, 2015 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at