15-52608967-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001385016.1(ATOSA):āc.1947A>Cā(p.Lys649Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,611,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001385016.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATOSA | NM_001385016.1 | c.1947A>C | p.Lys649Asn | missense_variant | 6/13 | ENST00000619572.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATOSA | ENST00000619572.5 | c.1947A>C | p.Lys649Asn | missense_variant | 6/13 | 1 | NM_001385016.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000105 AC: 26AN: 246918Hom.: 0 AF XY: 0.0000971 AC XY: 13AN XY: 133886
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1459368Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 725970
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2023 | The c.1947A>C (p.K649N) alteration is located in exon 6 (coding exon 5) of the FAM214A gene. This alteration results from a A to C substitution at nucleotide position 1947, causing the lysine (K) at amino acid position 649 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