rs2878802
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367773.1(ESYT2):c.2506-484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,232 control chromosomes in the GnomAD database, including 52,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.82 ( 52181 hom., cov: 33)
Consequence
ESYT2
NM_001367773.1 intron
NM_001367773.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.27
Genes affected
ESYT2 (HGNC:22211): (extended synaptotagmin 2) Enables calcium ion binding activity; identical protein binding activity; and phospholipid binding activity. Predicted to be involved in endocytosis; endoplasmic reticulum-plasma membrane tethering; and lipid transport. Located in endoplasmic reticulum-plasma membrane contact site. Is extrinsic component of cytoplasmic side of plasma membrane; integral component of plasma membrane; and intrinsic component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ESYT2 | NM_001367773.1 | c.2506-484G>A | intron_variant | ENST00000275418.13 | NP_001354702.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ESYT2 | ENST00000275418.13 | c.2506-484G>A | intron_variant | 5 | NM_001367773.1 | ENSP00000275418.8 | ||||
ESYT2 | ENST00000251527.10 | c.2443-484G>A | intron_variant | 1 | ENSP00000251527.6 | |||||
ESYT2 | ENST00000652148.1 | c.2587-484G>A | intron_variant | ENSP00000499020.1 | ||||||
ESYT2 | ENST00000435514.3 | n.1401-484G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.824 AC: 125408AN: 152114Hom.: 52160 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.824 AC: 125467AN: 152232Hom.: 52181 Cov.: 33 AF XY: 0.825 AC XY: 61360AN XY: 74420
GnomAD4 genome
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33
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61360
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74420
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3084
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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