X-54446192-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_004463.3(FGD1):c.2803A>G(p.Arg935Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000888 in 112,580 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R935R) has been classified as Likely benign.
Frequency
Consequence
NM_004463.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGD1 | NM_004463.3 | c.2803A>G | p.Arg935Gly | missense_variant | 18/18 | ENST00000375135.4 | |
TSR2 | NM_058163.3 | c.*1642T>C | 3_prime_UTR_variant | 5/5 | ENST00000375151.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGD1 | ENST00000375135.4 | c.2803A>G | p.Arg935Gly | missense_variant | 18/18 | 1 | NM_004463.3 | P1 | |
TSR2 | ENST00000375151.5 | c.*1642T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_058163.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000888 AC: 1AN: 112580Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34726
GnomAD4 exome Cov.: 31
GnomAD4 genome ? AF: 0.00000888 AC: 1AN: 112580Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34726
ClinVar
Submissions by phenotype
Aarskog syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at