12-90971846-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004950.5(EPYC):c.656G>A(p.Ser219Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000194 in 1,611,584 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S219T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004950.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPYC | NM_004950.5 | c.656G>A | p.Ser219Asn | missense_variant | Exon 5 of 7 | ENST00000261172.8 | NP_004941.2 | |
EPYC | XM_011538008.2 | c.473G>A | p.Ser158Asn | missense_variant | Exon 4 of 6 | XP_011536310.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151946Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000680 AC: 17AN: 249978Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135182
GnomAD4 exome AF: 0.000206 AC: 300AN: 1459638Hom.: 0 Cov.: 30 AF XY: 0.000208 AC XY: 151AN XY: 726132
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151946Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74206
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.656G>A (p.S219N) alteration is located in exon 5 (coding exon 4) of the EPYC gene. This alteration results from a G to A substitution at nucleotide position 656, causing the serine (S) at amino acid position 219 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