rs777764350
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015630.4(EPC2):āc.14C>Gā(p.Ser5Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000429 in 1,398,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S5F) has been classified as Uncertain significance.
Frequency
Consequence
NM_015630.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPC2 | ENST00000258484.11 | c.14C>G | p.Ser5Cys | missense_variant | Exon 1 of 14 | 1 | NM_015630.4 | ENSP00000258484.6 | ||
EPC2 | ENST00000409654.5 | c.14C>G | p.Ser5Cys | missense_variant | Exon 1 of 3 | 3 | ENSP00000387097.1 | |||
EPC2 | ENST00000457184.5 | c.-50-9C>G | intron_variant | Intron 1 of 4 | 5 | ENSP00000415543.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000626 AC: 1AN: 159746Hom.: 0 AF XY: 0.0000118 AC XY: 1AN XY: 85018
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1398888Hom.: 0 Cov.: 34 AF XY: 0.00000579 AC XY: 4AN XY: 690408
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at