chr15-52609223-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001385016.1(ATOSA):c.1691G>A(p.Cys564Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,611,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001385016.1 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 |
---|---|---|---|---|---|---|---|
ATOSA | NM_001385016.1 | c.1691G>A | p.Cys564Tyr | missense_variant | 6/13 | ENST00000619572.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATOSA | ENST00000619572.5 | c.1691G>A | p.Cys564Tyr | missense_variant | 6/13 | 1 | NM_001385016.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246176Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133806
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459528Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 726130
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.1691G>A (p.C564Y) alteration is located in exon 6 (coding exon 5) of the FAM214A gene. This alteration results from a G to A substitution at nucleotide position 1691, causing the cysteine (C) at amino acid position 564 to be replaced by a tyrosine (Y). 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