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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-65379537-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=65379537&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MAGI1",
"hgnc_id": 946,
"hgvs_c": "c.2719G>A",
"hgvs_p": "p.Glu907Lys",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001033057.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 40,
"alphamissense_prediction": null,
"alphamissense_score": 0.3502,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.24809011816978455,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1462,
"aa_ref": "E",
"aa_start": 907,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7851,
"cdna_start": 3329,
"cds_end": null,
"cds_length": 4389,
"cds_start": 2719,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001033057.2",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2719G>A",
"hgvs_p": "p.Glu907Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000402939.7",
"protein_coding": true,
"protein_id": "NP_001028229.1",
"strand": false,
"transcript": "NM_001033057.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1462,
"aa_ref": "E",
"aa_start": 907,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7851,
"cdna_start": 3329,
"cds_end": null,
"cds_length": 4389,
"cds_start": 2719,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000402939.7",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2719G>A",
"hgvs_p": "p.Glu907Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001033057.2",
"protein_coding": true,
"protein_id": "ENSP00000385450.2",
"strand": false,
"transcript": "ENST00000402939.7",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1287,
"aa_ref": "E",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7415,
"cdna_start": 2803,
"cds_end": null,
"cds_length": 3864,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000330909.12",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2803G>A",
"hgvs_p": "p.Glu935Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000331157.7",
"strand": false,
"transcript": "ENST00000330909.12",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1256,
"aa_ref": "E",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4791,
"cdna_start": 3045,
"cds_end": null,
"cds_length": 3771,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000483466.5",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2803G>A",
"hgvs_p": "p.Glu935Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420323.1",
"strand": false,
"transcript": "ENST00000483466.5",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1155,
"aa_ref": "E",
"aa_start": 600,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6225,
"cdna_start": 2408,
"cds_end": null,
"cds_length": 3468,
"cds_start": 1798,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000621418.4",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.1798G>A",
"hgvs_p": "p.Glu600Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477591.1",
"strand": false,
"transcript": "ENST00000621418.4",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 980,
"aa_ref": "E",
"aa_start": 628,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6398,
"cdna_start": 2492,
"cds_end": null,
"cds_length": 2943,
"cds_start": 1882,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000611645.4",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.1882G>A",
"hgvs_p": "p.Glu628Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480920.1",
"strand": false,
"transcript": "ENST00000611645.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 972,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000468159.1",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "n.779G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000468159.1",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1289,
"aa_ref": "E",
"aa_start": 936,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8030,
"cdna_start": 3416,
"cds_end": null,
"cds_length": 3870,
"cds_start": 2806,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001365903.2",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2806G>A",
"hgvs_p": "p.Glu936Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001352832.1",
"strand": false,
"transcript": "NM_001365903.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1288,
"aa_ref": "E",
"aa_start": 936,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8027,
"cdna_start": 3416,
"cds_end": null,
"cds_length": 3867,
"cds_start": 2806,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001365904.2",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2806G>A",
"hgvs_p": "p.Glu936Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001352833.1",
"strand": false,
"transcript": "NM_001365904.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1287,
"aa_ref": "E",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8024,
"cdna_start": 3413,
"cds_end": null,
"cds_length": 3864,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_015520.2",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2803G>A",
"hgvs_p": "p.Glu935Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_056335.1",
"strand": false,
"transcript": "NM_015520.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1257,
"aa_ref": "E",
"aa_start": 936,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6261,
"cdna_start": 3416,
"cds_end": null,
"cds_length": 3774,
"cds_start": 2806,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001365905.1",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2806G>A",
"hgvs_p": "p.Glu936Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001352834.1",
"strand": false,
"transcript": "NM_001365905.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1256,
"aa_ref": "E",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6258,
"cdna_start": 3413,
"cds_end": null,
"cds_length": 3771,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_004742.3",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2803G>A",
"hgvs_p": "p.Glu935Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_004733.2",
"strand": false,
"transcript": "NM_004742.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1160,
"aa_ref": "E",
"aa_start": 907,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3555,
"cdna_start": 2719,
"cds_end": null,
"cds_length": 3483,
"cds_start": 2719,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000497477.6",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2719G>A",
"hgvs_p": "p.Glu907Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424369.1",
"strand": false,
"transcript": "ENST00000497477.6",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1135,
"aa_ref": "E",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3694,
"cdna_start": 2445,
"cds_end": null,
"cds_length": 3408,
"cds_start": 2443,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000460329.6",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2443G>A",
"hgvs_p": "p.Glu815Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418862.2",
"strand": false,
"transcript": "ENST00000460329.6",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1131,
"aa_ref": "E",
"aa_start": 810,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4193,
"cdna_start": 2428,
"cds_end": null,
"cds_length": 3396,
"cds_start": 2428,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000463103.6",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2428G>A",
"hgvs_p": "p.Glu810Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418177.2",
"strand": false,
"transcript": "ENST00000463103.6",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1014,
"aa_ref": "E",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3045,
"cdna_start": 2077,
"cds_end": null,
"cds_length": 3045,
"cds_start": 2077,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000472257.5",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "c.2077G>A",
"hgvs_p": "p.Glu693Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420796.1",
"strand": false,
"transcript": "ENST00000472257.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000480729.1",
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"hgvs_c": "n.108G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000480729.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs143546019",
"effect": "missense_variant",
"frequency_reference_population": 0.000024847746,
"gene_hgnc_id": 946,
"gene_symbol": "MAGI1",
"gnomad_exomes_ac": 38,
"gnomad_exomes_af": 0.0000260698,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131427,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.65,
"pos": 65379537,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.098,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001033057.2"
}
]
}