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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: 3-65379345-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=65379345&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 65379345,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001033057.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2911G>A",
"hgvs_p": "p.Val971Met",
"transcript": "NM_001033057.2",
"protein_id": "NP_001028229.1",
"transcript_support_level": null,
"aa_start": 971,
"aa_end": null,
"aa_length": 1462,
"cds_start": 2911,
"cds_end": null,
"cds_length": 4389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000402939.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001033057.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2911G>A",
"hgvs_p": "p.Val971Met",
"transcript": "ENST00000402939.7",
"protein_id": "ENSP00000385450.2",
"transcript_support_level": 1,
"aa_start": 971,
"aa_end": null,
"aa_length": 1462,
"cds_start": 2911,
"cds_end": null,
"cds_length": 4389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001033057.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402939.7"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2995G>A",
"hgvs_p": "p.Val999Met",
"transcript": "ENST00000330909.12",
"protein_id": "ENSP00000331157.7",
"transcript_support_level": 1,
"aa_start": 999,
"aa_end": null,
"aa_length": 1287,
"cds_start": 2995,
"cds_end": null,
"cds_length": 3864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000330909.12"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2995G>A",
"hgvs_p": "p.Val999Met",
"transcript": "ENST00000483466.5",
"protein_id": "ENSP00000420323.1",
"transcript_support_level": 1,
"aa_start": 999,
"aa_end": null,
"aa_length": 1256,
"cds_start": 2995,
"cds_end": null,
"cds_length": 3771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483466.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.1990G>A",
"hgvs_p": "p.Val664Met",
"transcript": "ENST00000621418.4",
"protein_id": "ENSP00000477591.1",
"transcript_support_level": 1,
"aa_start": 664,
"aa_end": null,
"aa_length": 1155,
"cds_start": 1990,
"cds_end": null,
"cds_length": 3468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000621418.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2074G>A",
"hgvs_p": "p.Val692Met",
"transcript": "ENST00000611645.4",
"protein_id": "ENSP00000480920.1",
"transcript_support_level": 1,
"aa_start": 692,
"aa_end": null,
"aa_length": 980,
"cds_start": 2074,
"cds_end": null,
"cds_length": 2943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000611645.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "n.971G>A",
"hgvs_p": null,
"transcript": "ENST00000468159.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000468159.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2998G>A",
"hgvs_p": "p.Val1000Met",
"transcript": "NM_001365903.2",
"protein_id": "NP_001352832.1",
"transcript_support_level": null,
"aa_start": 1000,
"aa_end": null,
"aa_length": 1289,
"cds_start": 2998,
"cds_end": null,
"cds_length": 3870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365903.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2998G>A",
"hgvs_p": "p.Val1000Met",
"transcript": "NM_001365904.2",
"protein_id": "NP_001352833.1",
"transcript_support_level": null,
"aa_start": 1000,
"aa_end": null,
"aa_length": 1288,
"cds_start": 2998,
"cds_end": null,
"cds_length": 3867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365904.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2995G>A",
"hgvs_p": "p.Val999Met",
"transcript": "NM_015520.2",
"protein_id": "NP_056335.1",
"transcript_support_level": null,
"aa_start": 999,
"aa_end": null,
"aa_length": 1287,
"cds_start": 2995,
"cds_end": null,
"cds_length": 3864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015520.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2998G>A",
"hgvs_p": "p.Val1000Met",
"transcript": "NM_001365905.1",
"protein_id": "NP_001352834.1",
"transcript_support_level": null,
"aa_start": 1000,
"aa_end": null,
"aa_length": 1257,
"cds_start": 2998,
"cds_end": null,
"cds_length": 3774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365905.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2995G>A",
"hgvs_p": "p.Val999Met",
"transcript": "NM_004742.3",
"protein_id": "NP_004733.2",
"transcript_support_level": null,
"aa_start": 999,
"aa_end": null,
"aa_length": 1256,
"cds_start": 2995,
"cds_end": null,
"cds_length": 3771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004742.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2911G>A",
"hgvs_p": "p.Val971Met",
"transcript": "ENST00000497477.6",
"protein_id": "ENSP00000424369.1",
"transcript_support_level": 5,
"aa_start": 971,
"aa_end": null,
"aa_length": 1160,
"cds_start": 2911,
"cds_end": null,
"cds_length": 3483,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000497477.6"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2635G>A",
"hgvs_p": "p.Val879Met",
"transcript": "ENST00000460329.6",
"protein_id": "ENSP00000418862.2",
"transcript_support_level": 5,
"aa_start": 879,
"aa_end": null,
"aa_length": 1135,
"cds_start": 2635,
"cds_end": null,
"cds_length": 3408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000460329.6"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2620G>A",
"hgvs_p": "p.Val874Met",
"transcript": "ENST00000463103.6",
"protein_id": "ENSP00000418177.2",
"transcript_support_level": 5,
"aa_start": 874,
"aa_end": null,
"aa_length": 1131,
"cds_start": 2620,
"cds_end": null,
"cds_length": 3396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000463103.6"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "c.2269G>A",
"hgvs_p": "p.Val757Met",
"transcript": "ENST00000472257.5",
"protein_id": "ENSP00000420796.1",
"transcript_support_level": 5,
"aa_start": 757,
"aa_end": null,
"aa_length": 1014,
"cds_start": 2269,
"cds_end": null,
"cds_length": 3045,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472257.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"hgvs_c": "n.300G>A",
"hgvs_p": null,
"transcript": "ENST00000480729.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000480729.1"
}
],
"gene_symbol": "MAGI1",
"gene_hgnc_id": 946,
"dbsnp": "rs149468264",
"frequency_reference_population": 0.000045173547,
"hom_count_reference_population": 0,
"allele_count_reference_population": 66,
"gnomad_exomes_af": 0.0000451735,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 66,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7447658181190491,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.381,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9328,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.779,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001033057.2",
"gene_symbol": "MAGI1",
"hgnc_id": 946,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2911G>A",
"hgvs_p": "p.Val971Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}