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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: 12-42237690-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=42237690&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 42237690,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001190979.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "NM_005748.6",
"protein_id": "NP_005739.2",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 180,
"cds_start": 61,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000534854.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005748.6"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "ENST00000534854.7",
"protein_id": "ENSP00000439256.2",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 180,
"cds_start": 61,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005748.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000534854.7"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "ENST00000327791.8",
"protein_id": "ENSP00000328004.5",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 204,
"cds_start": 61,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327791.8"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "NM_001190979.3",
"protein_id": "NP_001177908.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 204,
"cds_start": 61,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190979.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "NM_001190980.3",
"protein_id": "NP_001177909.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 117,
"cds_start": 61,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190980.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "ENST00000555248.2",
"protein_id": "ENSP00000451626.2",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 117,
"cds_start": 61,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555248.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "XM_011537728.4",
"protein_id": "XP_011536030.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 238,
"cds_start": 61,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537728.4"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Gly21Ser",
"transcript": "XM_017018670.3",
"protein_id": "XP_016874159.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 120,
"cds_start": 61,
"cds_end": null,
"cds_length": 363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018670.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.-67G>A",
"hgvs_p": null,
"transcript": "NM_001320080.2",
"protein_id": "NP_001307009.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": null,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320080.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.-57G>A",
"hgvs_p": null,
"transcript": "ENST00000548917.1",
"protein_id": "ENSP00000447686.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 33,
"cds_start": null,
"cds_end": null,
"cds_length": 102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.-67G>A",
"hgvs_p": null,
"transcript": "XM_047428048.1",
"protein_id": "XP_047284004.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": null,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428048.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.-67G>A",
"hgvs_p": null,
"transcript": "XM_047428049.1",
"protein_id": "XP_047284005.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": null,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428049.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.26+465G>A",
"hgvs_p": null,
"transcript": "ENST00000880607.1",
"protein_id": "ENSP00000550666.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 162,
"cds_start": null,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880607.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.26+465G>A",
"hgvs_p": null,
"transcript": "NM_001190977.3",
"protein_id": "NP_001177906.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190977.3"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "c.26+465G>A",
"hgvs_p": null,
"transcript": "ENST00000380790.4",
"protein_id": "ENSP00000370167.4",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000380790.4"
},
{
"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": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.129G>A",
"hgvs_p": null,
"transcript": "ENST00000541702.2",
"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": "ENST00000541702.2"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.61G>A",
"hgvs_p": null,
"transcript": "ENST00000546726.5",
"protein_id": "ENSP00000447863.1",
"transcript_support_level": 3,
"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": "ENST00000546726.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.94G>A",
"hgvs_p": null,
"transcript": "ENST00000546782.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000546782.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.61G>A",
"hgvs_p": null,
"transcript": "ENST00000547254.5",
"protein_id": "ENSP00000448312.1",
"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": "ENST00000547254.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.61G>A",
"hgvs_p": null,
"transcript": "ENST00000547351.5",
"protein_id": "ENSP00000450394.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000547351.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.111G>A",
"hgvs_p": null,
"transcript": "ENST00000547724.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000547724.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YAF2",
"gene_hgnc_id": 17363,
"hgvs_c": "n.61G>A",
"hgvs_p": null,
"transcript": "ENST00000551268.5",
"protein_id": "ENSP00000448291.1",
"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": "ENST00000551268.5"
},
{
"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": 5,
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"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.02621e-7,
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"gnomad_exomes_ac": 1,
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"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2928,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.13,
"phylop100way_prediction": "Uncertain_significance",
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"mitotip_score": null,
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"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
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"pathogenic_score": 2,
"criteria": [
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],
"verdict": "Uncertain_significance",
"transcript": "NM_001190979.3",
"gene_symbol": "YAF2",
"hgnc_id": 17363,
"effects": [
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],
"inheritance_mode": "AD",
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],
"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
}