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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: 3-49684430-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49684430&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49684430,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001393581.1",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1900A>C",
"hgvs_p": "p.Asn634His",
"transcript": "NM_020998.4",
"protein_id": "NP_066278.3",
"transcript_support_level": null,
"aa_start": 634,
"aa_end": null,
"aa_length": 725,
"cds_start": 1900,
"cds_end": null,
"cds_length": 2178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000449682.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020998.4"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1900A>C",
"hgvs_p": "p.Asn634His",
"transcript": "ENST00000449682.3",
"protein_id": "ENSP00000414287.2",
"transcript_support_level": 1,
"aa_start": 634,
"aa_end": null,
"aa_length": 725,
"cds_start": 1900,
"cds_end": null,
"cds_length": 2178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020998.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449682.3"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1936A>C",
"hgvs_p": "p.Asn646His",
"transcript": "NM_001393581.1",
"protein_id": "NP_001380510.1",
"transcript_support_level": null,
"aa_start": 646,
"aa_end": null,
"aa_length": 737,
"cds_start": 1936,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393581.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1900A>C",
"hgvs_p": "p.Asn634His",
"transcript": "NM_001393582.1",
"protein_id": "NP_001380511.1",
"transcript_support_level": null,
"aa_start": 634,
"aa_end": null,
"aa_length": 706,
"cds_start": 1900,
"cds_end": null,
"cds_length": 2121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393582.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1810A>C",
"hgvs_p": "p.Asn604His",
"transcript": "NM_001393583.1",
"protein_id": "NP_001380512.1",
"transcript_support_level": null,
"aa_start": 604,
"aa_end": null,
"aa_length": 695,
"cds_start": 1810,
"cds_end": null,
"cds_length": 2088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393583.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1765A>C",
"hgvs_p": "p.Asn589His",
"transcript": "NM_001393584.1",
"protein_id": "NP_001380513.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 680,
"cds_start": 1765,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393584.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1600A>C",
"hgvs_p": "p.Asn534His",
"transcript": "NM_001393585.1",
"protein_id": "NP_001380514.1",
"transcript_support_level": null,
"aa_start": 534,
"aa_end": null,
"aa_length": 625,
"cds_start": 1600,
"cds_end": null,
"cds_length": 1878,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393585.1"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.307A>C",
"hgvs_p": "p.Asn103His",
"transcript": "ENST00000448220.5",
"protein_id": "ENSP00000394756.1",
"transcript_support_level": 5,
"aa_start": 103,
"aa_end": null,
"aa_length": 194,
"cds_start": 307,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448220.5"
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1936A>C",
"hgvs_p": "p.Asn646His",
"transcript": "XM_017006460.3",
"protein_id": "XP_016861949.1",
"transcript_support_level": null,
"aa_start": 646,
"aa_end": null,
"aa_length": 718,
"cds_start": 1936,
"cds_end": null,
"cds_length": 2157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006460.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1821-33A>C",
"hgvs_p": null,
"transcript": "XM_047448158.1",
"protein_id": "XP_047304114.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 655,
"cds_start": null,
"cds_end": null,
"cds_length": 1968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448158.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "c.1686-33A>C",
"hgvs_p": null,
"transcript": "XM_047448159.1",
"protein_id": "XP_047304115.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 610,
"cds_start": null,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448159.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.1955A>C",
"hgvs_p": null,
"transcript": "ENST00000479115.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000479115.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.773A>C",
"hgvs_p": null,
"transcript": "ENST00000484144.1",
"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": "retained_intron",
"feature": "ENST00000484144.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.3822A>C",
"hgvs_p": null,
"transcript": "ENST00000488350.6",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000488350.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.1676A>C",
"hgvs_p": null,
"transcript": "ENST00000492329.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000492329.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.666A>C",
"hgvs_p": null,
"transcript": "ENST00000493836.5",
"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": "retained_intron",
"feature": "ENST00000493836.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"hgvs_c": "n.2597-33A>C",
"hgvs_p": null,
"transcript": "NR_146060.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_146060.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259970",
"gene_hgnc_id": null,
"hgvs_c": "n.*50A>C",
"hgvs_p": null,
"transcript": "ENST00000563780.1",
"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": "retained_intron",
"feature": "ENST00000563780.1"
}
],
"gene_symbol": "MST1",
"gene_hgnc_id": 7380,
"dbsnp": null,
"frequency_reference_population": 0.0000068439335,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000684393,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.45302096009254456,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.463,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0755,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.552,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001393581.1",
"gene_symbol": "MST1",
"hgnc_id": 7380,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.1936A>C",
"hgvs_p": "p.Asn646His"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000563780.1",
"gene_symbol": "ENSG00000259970",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*50A>C",
"hgvs_p": null
}
],
"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
}