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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: 4-78911632-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=78911632&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 78911632,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_198892.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.3085T>A",
"hgvs_p": "p.Ser1029Thr",
"transcript": "NM_198892.2",
"protein_id": "NP_942595.1",
"transcript_support_level": null,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1161,
"cds_start": 3085,
"cds_end": null,
"cds_length": 3486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000502613.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198892.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.3085T>A",
"hgvs_p": "p.Ser1029Thr",
"transcript": "ENST00000502613.3",
"protein_id": "ENSP00000424668.2",
"transcript_support_level": 1,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1161,
"cds_start": 3085,
"cds_end": null,
"cds_length": 3486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198892.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502613.3"
},
{
"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": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*782+3578A>T",
"hgvs_p": null,
"transcript": "ENST00000342820.10",
"protein_id": "ENSP00000344203.6",
"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": "nonsense_mediated_decay",
"feature": "ENST00000342820.10"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*792+3578A>T",
"hgvs_p": null,
"transcript": "ENST00000512760.5",
"protein_id": "ENSP00000426875.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000512760.5"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.2974T>A",
"hgvs_p": "p.Ser992Thr",
"transcript": "NM_001419799.1",
"protein_id": "NP_001406728.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1124,
"cds_start": 2974,
"cds_end": null,
"cds_length": 3375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001419799.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.2974T>A",
"hgvs_p": "p.Ser992Thr",
"transcript": "ENST00000858772.1",
"protein_id": "ENSP00000528831.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1124,
"cds_start": 2974,
"cds_end": null,
"cds_length": 3375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858772.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.2917T>A",
"hgvs_p": "p.Ser973Thr",
"transcript": "XM_047415931.1",
"protein_id": "XP_047271887.1",
"transcript_support_level": null,
"aa_start": 973,
"aa_end": null,
"aa_length": 1105,
"cds_start": 2917,
"cds_end": null,
"cds_length": 3318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047415931.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.2845T>A",
"hgvs_p": "p.Ser949Thr",
"transcript": "XM_017008381.2",
"protein_id": "XP_016863870.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2845,
"cds_end": null,
"cds_length": 3246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008381.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"hgvs_c": "c.2845T>A",
"hgvs_p": "p.Ser949Thr",
"transcript": "XM_047415932.1",
"protein_id": "XP_047271888.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2845,
"cds_end": null,
"cds_length": 3246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047415932.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*557A>T",
"hgvs_p": null,
"transcript": "ENST00000511594.5",
"protein_id": "ENSP00000425080.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000511594.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*557A>T",
"hgvs_p": null,
"transcript": "ENST00000511594.5",
"protein_id": "ENSP00000425080.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000511594.5"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.1288+3578A>T",
"hgvs_p": null,
"transcript": "XR_007096371.1",
"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": "XR_007096371.1"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.1288+3578A>T",
"hgvs_p": null,
"transcript": "XR_007096372.1",
"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": "XR_007096372.1"
},
{
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.1128-5471A>T",
"hgvs_p": null,
"transcript": "XR_938694.4",
"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": "XR_938694.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "c.*8907A>T",
"hgvs_p": null,
"transcript": "NM_001040202.2",
"protein_id": "NP_001035292.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": null,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000512733.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040202.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "c.*8907A>T",
"hgvs_p": null,
"transcript": "ENST00000512733.5",
"protein_id": "ENSP00000421981.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": null,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001040202.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512733.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "c.*8907A>T",
"hgvs_p": null,
"transcript": "NM_001350105.2",
"protein_id": "NP_001337034.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350105.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "c.*8907A>T",
"hgvs_p": null,
"transcript": "NM_001350106.2",
"protein_id": "NP_001337035.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350106.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*246A>T",
"hgvs_p": null,
"transcript": "NR_146462.2",
"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_146462.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*246A>T",
"hgvs_p": null,
"transcript": "NR_146463.2",
"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_146463.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*246A>T",
"hgvs_p": null,
"transcript": "NR_146464.2",
"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_146464.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAQR3",
"gene_hgnc_id": 30130,
"hgvs_c": "n.*246A>T",
"hgvs_p": null,
"transcript": "NR_146465.2",
"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_146465.2"
}
],
"gene_symbol": "BMP2K",
"gene_hgnc_id": 18041,
"dbsnp": "rs755015481",
"frequency_reference_population": 0.00001363313,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000129986,
"gnomad_genomes_af": 0.0000197337,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4003705680370331,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.513,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3209,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.182,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_198892.2",
"gene_symbol": "BMP2K",
"hgnc_id": 18041,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3085T>A",
"hgvs_p": "p.Ser1029Thr"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000511594.5",
"gene_symbol": "PAQR3",
"hgnc_id": 30130,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*557A>T",
"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
}