chr2-33584933-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015475.5(FAM98A):c.1400G>A(p.Arg467His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000245 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015475.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM98A | NM_015475.5 | c.1400G>A | p.Arg467His | missense_variant | 8/8 | ENST00000238823.13 | |
FAM98A | NM_001304538.2 | c.815G>A | p.Arg272His | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM98A | ENST00000238823.13 | c.1400G>A | p.Arg467His | missense_variant | 8/8 | 1 | NM_015475.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251364Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135876
GnomAD4 exome AF: 0.000259 AC: 378AN: 1461798Hom.: 0 Cov.: 32 AF XY: 0.000270 AC XY: 196AN XY: 727210
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.1400G>A (p.R467H) alteration is located in exon 8 (coding exon 8) of the FAM98A gene. This alteration results from a G to A substitution at nucleotide position 1400, causing the arginine (R) at amino acid position 467 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at