rs200542541
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001370298.3(FGD4):c.1923-7A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,590,516 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001370298.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGD4 | NM_001370298.3 | c.1923-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000534526.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGD4 | ENST00000534526.7 | c.1923-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001370298.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000268 AC: 66AN: 245862Hom.: 0 AF XY: 0.000271 AC XY: 36AN XY: 132934
GnomAD4 exome AF: 0.000181 AC: 260AN: 1438528Hom.: 2 Cov.: 28 AF XY: 0.000201 AC XY: 144AN XY: 716378
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74220
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | FGD4: PM2, BP4 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 06, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at