chr22-38586190-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001013647.2(FAM227A):c.1648G>A(p.Gly550Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000258 in 1,551,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013647.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM227A | ENST00000535113.7 | c.1648G>A | p.Gly550Arg | missense_variant | Exon 17 of 17 | 5 | NM_001013647.2 | ENSP00000445093.1 | ||
FAM227A | ENST00000355830.11 | c.1722G>A | p.Lys574Lys | synonymous_variant | Exon 17 of 19 | 5 | ENSP00000348086.7 | |||
FAM227A | ENST00000540952.6 | c.1722G>A | p.Lys574Lys | synonymous_variant | Exon 17 of 17 | 5 | ENSP00000493504.1 | |||
FAM227A | ENST00000543828.1 | n.-45G>A | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1398954Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 690002
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1648G>A (p.G550R) alteration is located in exon 17 (coding exon 16) of the FAM227A gene. This alteration results from a G to A substitution at nucleotide position 1648, causing the glycine (G) at amino acid position 550 to be replaced by an arginine (R). 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