11-95090165-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015036.3(ENDOD1):c.238G>A(p.Ala80Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000337 in 1,454,598 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
ENDOD1
NM_015036.3 missense
NM_015036.3 missense
Scores
8
8
3
Clinical Significance
Conservation
PhyloP100: 7.09
Genes affected
ENDOD1 (HGNC:29129): (endonuclease domain containing 1) Predicted to enable endonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Located in extracellular exosome and 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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENDOD1 | NM_015036.3 | c.238G>A | p.Ala80Thr | missense_variant | 1/2 | ENST00000278505.5 | NP_055851.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENDOD1 | ENST00000278505.5 | c.238G>A | p.Ala80Thr | missense_variant | 1/2 | 1 | NM_015036.3 | ENSP00000278505 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152230Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000312 AC: 3AN: 96248Hom.: 0 AF XY: 0.0000186 AC XY: 1AN XY: 53670
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GnomAD4 exome AF: 0.0000169 AC: 22AN: 1302250Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 8AN XY: 636154
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GnomAD4 genome AF: 0.000177 AC: 27AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 8AN XY: 74498
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.238G>A (p.A80T) alteration is located in exon 1 (coding exon 1) of the ENDOD1 gene. This alteration results from a G to A substitution at nucleotide position 238, causing the alanine (A) at amino acid position 80 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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