2-16552952-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030797.4(CYRIA):c.956G>A(p.Arg319Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000275 in 1,456,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030797.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
CYRIA | ENST00000381323.7 | c.956G>A | p.Arg319Gln | missense_variant | Exon 12 of 12 | 1 | NM_030797.4 | ENSP00000370724.3 | ||
CYRIA | ENST00000406434.5 | c.956G>A | p.Arg319Gln | missense_variant | Exon 13 of 13 | 5 | ENSP00000384771.1 | |||
ENSG00000237633 | ENST00000648675.1 | n.979+209C>T | intron_variant | Intron 6 of 6 | ||||||
ENSG00000237633 | ENST00000667231.1 | n.627+209C>T | intron_variant | Intron 5 of 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250734Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135492
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1456100Hom.: 0 Cov.: 27 AF XY: 0.00000414 AC XY: 3AN XY: 724870
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.956G>A (p.R319Q) alteration is located in exon 1 (coding exon 1) of the FAM49A gene. This alteration results from a G to A substitution at nucleotide position 956, causing the arginine (R) at amino acid position 319 to be replaced by a glutamine (Q). 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