19-55691799-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001130072.2(EPN1):āc.808G>Cā(p.Ala270Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,332 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 Likely benign (ā ).
Frequency
Consequence
NM_001130072.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPN1 | NM_001130072.2 | c.808G>C | p.Ala270Pro | missense_variant | 7/11 | ENST00000270460.11 | |
EPN1 | NM_001130071.2 | c.1066G>C | p.Ala356Pro | missense_variant | 7/11 | ||
EPN1 | NM_001321263.2 | c.808G>C | p.Ala270Pro | missense_variant | 7/11 | ||
EPN1 | NM_013333.4 | c.733G>C | p.Ala245Pro | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPN1 | ENST00000270460.11 | c.808G>C | p.Ala270Pro | missense_variant | 7/11 | 2 | NM_001130072.2 | P3 | |
EPN1 | ENST00000411543.6 | c.1066G>C | p.Ala356Pro | missense_variant | 7/11 | 1 | |||
EPN1 | ENST00000085079.11 | c.733G>C | p.Ala245Pro | missense_variant | 6/10 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 244538Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133066
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460276Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726456
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at