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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: 3-160417798-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=160417798&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 160417798,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_005496.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "NM_001002800.3",
"protein_id": "NP_001002800.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"cds_end": null,
"cds_length": 3867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357388.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001002800.3"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "ENST00000357388.8",
"protein_id": "ENSP00000349961.3",
"transcript_support_level": 1,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"cds_end": null,
"cds_length": 3867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001002800.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357388.8"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "ENST00000344722.5",
"protein_id": "ENSP00000341382.5",
"transcript_support_level": 1,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"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": "ENST00000344722.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.952+20434C>A",
"hgvs_p": null,
"transcript": "ENST00000483754.1",
"protein_id": "ENSP00000456272.1",
"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": "ENST00000483754.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "NM_005496.3",
"protein_id": "NP_005487.3",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"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_005496.3"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "ENST00000937686.1",
"protein_id": "ENSP00000607745.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"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": "ENST00000937686.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1438G>T",
"hgvs_p": "p.Glu480*",
"transcript": "NM_001288753.2",
"protein_id": "NP_001275682.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 1263,
"cds_start": 1438,
"cds_end": null,
"cds_length": 3792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001288753.2"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1438G>T",
"hgvs_p": "p.Glu480*",
"transcript": "ENST00000469762.5",
"protein_id": "ENSP00000417964.1",
"transcript_support_level": 2,
"aa_start": 480,
"aa_end": null,
"aa_length": 1263,
"cds_start": 1438,
"cds_end": null,
"cds_length": 3792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000469762.5"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "ENST00000462787.5",
"protein_id": "ENSP00000420734.1",
"transcript_support_level": 2,
"aa_start": 505,
"aa_end": null,
"aa_length": 1230,
"cds_start": 1513,
"cds_end": null,
"cds_length": 3693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000462787.5"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1321G>T",
"hgvs_p": "p.Glu441*",
"transcript": "ENST00000937687.1",
"protein_id": "ENSP00000607746.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 1224,
"cds_start": 1321,
"cds_end": null,
"cds_length": 3675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937687.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*",
"transcript": "XM_011512311.3",
"protein_id": "XP_011510613.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 1288,
"cds_start": 1513,
"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": "XM_011512311.3"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1297G>T",
"hgvs_p": "p.Glu433*",
"transcript": "XM_011512312.3",
"protein_id": "XP_011510614.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 1216,
"cds_start": 1297,
"cds_end": null,
"cds_length": 3651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512312.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1437+1383G>T",
"hgvs_p": null,
"transcript": "ENST00000937685.1",
"protein_id": "ENSP00000607744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": null,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937685.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1437+1383G>T",
"hgvs_p": null,
"transcript": "ENST00000937688.1",
"protein_id": "ENSP00000607747.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": null,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937688.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "c.1437+1383G>T",
"hgvs_p": null,
"transcript": "XM_006713459.5",
"protein_id": "XP_006713522.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": null,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006713459.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "n.736G>T",
"hgvs_p": null,
"transcript": "ENST00000462668.5",
"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": "ENST00000462668.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "n.*821G>T",
"hgvs_p": null,
"transcript": "ENST00000469858.5",
"protein_id": "ENSP00000418434.1",
"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": "ENST00000469858.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "n.175G>T",
"hgvs_p": null,
"transcript": "ENST00000484799.1",
"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": "ENST00000484799.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"hgvs_c": "n.*821G>T",
"hgvs_p": null,
"transcript": "ENST00000469858.5",
"protein_id": "ENSP00000418434.1",
"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": "ENST00000469858.5"
},
{
"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": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.1147+20434C>A",
"hgvs_p": null,
"transcript": "NR_148401.1",
"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": "NR_148401.1"
},
{
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.1077+20434C>A",
"hgvs_p": null,
"transcript": "NR_148402.1",
"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": "NR_148402.1"
},
{
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.1344+20434C>A",
"hgvs_p": null,
"transcript": "NR_148403.1",
"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": "NR_148403.1"
}
],
"gene_symbol": "SMC4",
"gene_hgnc_id": 14013,
"dbsnp": "rs1236643072",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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_005496.3",
"gene_symbol": "SMC4",
"hgnc_id": 14013,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1513G>T",
"hgvs_p": "p.Glu505*"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000483754.1",
"gene_symbol": "TRIM59-IFT80",
"hgnc_id": 56756,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.952+20434C>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}