22-38599770-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001013647.2(FAM227A):c.1373G>A(p.Ser458Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000406 in 1,550,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/18 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM227A | ENST00000535113.7 | c.1373G>A | p.Ser458Asn | missense_variant | Exon 14 of 17 | 5 | NM_001013647.2 | ENSP00000445093.1 | ||
FAM227A | ENST00000355830.11 | c.1373G>A | p.Ser458Asn | missense_variant | Exon 14 of 19 | 5 | ENSP00000348086.7 | |||
FAM227A | ENST00000540952.6 | c.1373G>A | p.Ser458Asn | missense_variant | Exon 14 of 17 | 5 | ENSP00000493504.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000837 AC: 13AN: 155402Hom.: 0 AF XY: 0.000134 AC XY: 11AN XY: 82324
GnomAD4 exome AF: 0.0000408 AC: 57AN: 1398756Hom.: 0 Cov.: 31 AF XY: 0.0000464 AC XY: 32AN XY: 689880
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152098Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1373G>A (p.S458N) alteration is located in exon 14 (coding exon 13) of the FAM227A gene. This alteration results from a G to A substitution at nucleotide position 1373, causing the serine (S) at amino acid position 458 to be replaced by an asparagine (N). 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