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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: 1-32780128-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=32780128&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 32780128,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003680.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1291A>G",
"hgvs_p": "p.Met431Val",
"transcript": "NM_003680.4",
"protein_id": "NP_003671.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 528,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373477.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003680.4"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1291A>G",
"hgvs_p": "p.Met431Val",
"transcript": "ENST00000373477.9",
"protein_id": "ENSP00000362576.4",
"transcript_support_level": 1,
"aa_start": 431,
"aa_end": null,
"aa_length": 528,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003680.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373477.9"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1378A>G",
"hgvs_p": "p.Met460Val",
"transcript": "ENST00000906066.1",
"protein_id": "ENSP00000576125.1",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 557,
"cds_start": 1378,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906066.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1288A>G",
"hgvs_p": "p.Met430Val",
"transcript": "ENST00000918766.1",
"protein_id": "ENSP00000588825.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 527,
"cds_start": 1288,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918766.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1288A>G",
"hgvs_p": "p.Met430Val",
"transcript": "ENST00000918768.1",
"protein_id": "ENSP00000588827.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 527,
"cds_start": 1288,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918768.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1291A>G",
"hgvs_p": "p.Met431Val",
"transcript": "ENST00000956435.1",
"protein_id": "ENSP00000626494.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 524,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956435.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1291A>G",
"hgvs_p": "p.Met431Val",
"transcript": "ENST00000906068.1",
"protein_id": "ENSP00000576127.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 506,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906068.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1210A>G",
"hgvs_p": "p.Met404Val",
"transcript": "ENST00000906065.1",
"protein_id": "ENSP00000576124.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 501,
"cds_start": 1210,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906065.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1198A>G",
"hgvs_p": "p.Met400Val",
"transcript": "ENST00000918767.1",
"protein_id": "ENSP00000588826.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 497,
"cds_start": 1198,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918767.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1144A>G",
"hgvs_p": "p.Met382Val",
"transcript": "ENST00000675785.2",
"protein_id": "ENSP00000502019.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 479,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675785.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1117A>G",
"hgvs_p": "p.Met373Val",
"transcript": "ENST00000906067.1",
"protein_id": "ENSP00000576126.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 470,
"cds_start": 1117,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906067.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1069A>G",
"hgvs_p": "p.Met357Val",
"transcript": "ENST00000906064.1",
"protein_id": "ENSP00000576123.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 454,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906064.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.976A>G",
"hgvs_p": "p.Met326Val",
"transcript": "ENST00000918770.1",
"protein_id": "ENSP00000588829.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 423,
"cds_start": 976,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918770.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.895A>G",
"hgvs_p": "p.Met299Val",
"transcript": "ENST00000918769.1",
"protein_id": "ENSP00000588828.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 396,
"cds_start": 895,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918769.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.838A>G",
"hgvs_p": "p.Met280Val",
"transcript": "ENST00000906069.1",
"protein_id": "ENSP00000576128.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 377,
"cds_start": 838,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906069.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.661A>G",
"hgvs_p": "p.Met221Val",
"transcript": "XM_011542347.3",
"protein_id": "XP_011540649.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 318,
"cds_start": 661,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542347.3"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.1207A>G",
"hgvs_p": null,
"transcript": "ENST00000469100.5",
"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": "ENST00000469100.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.758A>G",
"hgvs_p": null,
"transcript": "ENST00000478828.1",
"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": "ENST00000478828.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.1601A>G",
"hgvs_p": null,
"transcript": "ENST00000487404.5",
"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": "ENST00000487404.5"
},
{
"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": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.584A>G",
"hgvs_p": null,
"transcript": "ENST00000490826.1",
"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": "ENST00000490826.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.*839A>G",
"hgvs_p": null,
"transcript": "ENST00000674629.1",
"protein_id": "ENSP00000502470.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000674629.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.*1251A>G",
"hgvs_p": null,
"transcript": "ENST00000674654.1",
"protein_id": "ENSP00000501729.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000674654.1"
},
{
"aa_ref": null,
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"canonical": false,
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{
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{
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{
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"3_prime_UTR_variant"
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],
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"dbsnp": "rs149620809",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8649599552154541,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": 0.713,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.345,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.659,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003680.4",
"gene_symbol": "YARS1",
"hgnc_id": 12840,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1291A>G",
"hgvs_p": "p.Met431Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}