17-50536650-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_017957.3(EPN3):c.94C>T(p.Pro32Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000658 in 152,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
EPN3
NM_017957.3 missense
NM_017957.3 missense
Scores
9
6
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.12
Genes affected
EPN3 (HGNC:18235): (epsin 3) Predicted to enable clathrin binding activity and phospholipid binding activity. Predicted to be involved in endocytosis. Located in clathrin-coated vesicle; nucleoplasm; and perinuclear region of cytoplasm. Is extrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.785
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPN3 | NM_017957.3 | c.94C>T | p.Pro32Ser | missense_variant | 2/10 | ENST00000268933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPN3 | ENST00000268933.8 | c.94C>T | p.Pro32Ser | missense_variant | 2/10 | 2 | NM_017957.3 | P1 | |
ENST00000654456.1 | n.482+1277G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152004Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 34
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152004Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74244
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D;D;.
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D;D;.
Sift4G
Pathogenic
D;D;D;D;D;D
Polyphen
D;.;.;.;.;.
Vest4
MutPred
Loss of catalytic residue at N30 (P = 0.0528);Loss of catalytic residue at N30 (P = 0.0528);Loss of catalytic residue at N30 (P = 0.0528);Loss of catalytic residue at N30 (P = 0.0528);Loss of catalytic residue at N30 (P = 0.0528);Loss of catalytic residue at N30 (P = 0.0528);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at