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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: 20-50935214-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=50935214&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 50935214,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001317034.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.701G>A",
"hgvs_p": "p.Arg234His",
"transcript": "NM_003859.3",
"protein_id": "NP_003850.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 260,
"cds_start": 701,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371588.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003859.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.701G>A",
"hgvs_p": "p.Arg234His",
"transcript": "ENST00000371588.10",
"protein_id": "ENSP00000360644.5",
"transcript_support_level": 1,
"aa_start": 234,
"aa_end": null,
"aa_length": 260,
"cds_start": 701,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003859.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371588.10"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261His",
"transcript": "ENST00000371582.8",
"protein_id": "ENSP00000360638.4",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 287,
"cds_start": 782,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371582.8"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.*156G>A",
"hgvs_p": null,
"transcript": "ENST00000466152.5",
"protein_id": "ENSP00000507119.1",
"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": "ENST00000466152.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.*156G>A",
"hgvs_p": null,
"transcript": "ENST00000466152.5",
"protein_id": "ENSP00000507119.1",
"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": "ENST00000466152.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.806G>A",
"hgvs_p": "p.Arg269His",
"transcript": "NM_001317034.1",
"protein_id": "NP_001303963.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 295,
"cds_start": 806,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317034.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.806G>A",
"hgvs_p": "p.Arg269His",
"transcript": "ENST00000371584.9",
"protein_id": "ENSP00000360640.5",
"transcript_support_level": 5,
"aa_start": 269,
"aa_end": null,
"aa_length": 295,
"cds_start": 806,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371584.9"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261His",
"transcript": "NM_001317035.1",
"protein_id": "NP_001303964.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 287,
"cds_start": 782,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317035.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.698G>A",
"hgvs_p": "p.Arg233His",
"transcript": "ENST00000970159.1",
"protein_id": "ENSP00000640218.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 259,
"cds_start": 698,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970159.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.665G>A",
"hgvs_p": "p.Arg222His",
"transcript": "ENST00000922811.1",
"protein_id": "ENSP00000592870.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 248,
"cds_start": 665,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922811.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.632G>A",
"hgvs_p": "p.Arg211His",
"transcript": "NM_001317036.1",
"protein_id": "NP_001303965.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 237,
"cds_start": 632,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317036.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000858753.1",
"protein_id": "ENSP00000528812.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 228,
"cds_start": 605,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858753.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.536G>A",
"hgvs_p": "p.Arg179His",
"transcript": "ENST00000858754.1",
"protein_id": "ENSP00000528813.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 205,
"cds_start": 536,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858754.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.368G>A",
"hgvs_p": "p.Arg123His",
"transcript": "ENST00000922813.1",
"protein_id": "ENSP00000592872.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 149,
"cds_start": 368,
"cds_end": null,
"cds_length": 450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922813.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.317G>A",
"hgvs_p": "p.Arg106His",
"transcript": "ENST00000683466.1",
"protein_id": "ENSP00000507404.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 132,
"cds_start": 317,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000683466.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "c.299G>A",
"hgvs_p": "p.Arg100His",
"transcript": "ENST00000922812.1",
"protein_id": "ENSP00000592871.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 126,
"cds_start": 299,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922812.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.471G>A",
"hgvs_p": null,
"transcript": "ENST00000494752.1",
"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": "ENST00000494752.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.1957G>A",
"hgvs_p": null,
"transcript": "ENST00000682366.1",
"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": "retained_intron",
"feature": "ENST00000682366.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.1181G>A",
"hgvs_p": null,
"transcript": "ENST00000682713.1",
"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": "retained_intron",
"feature": "ENST00000682713.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.*216G>A",
"hgvs_p": null,
"transcript": "ENST00000683048.1",
"protein_id": "ENSP00000506986.1",
"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": "ENST00000683048.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.1472G>A",
"hgvs_p": null,
"transcript": "ENST00000684193.1",
"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": "retained_intron",
"feature": "ENST00000684193.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM1",
"gene_hgnc_id": 3005,
"hgvs_c": "n.732G>A",
"hgvs_p": null,
"transcript": "NR_133648.2",
"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_133648.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
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{
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{
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],
"gene_symbol": "DPM1",
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"dbsnp": "rs760322056",
"frequency_reference_population": 0.000007469069,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000755221,
"gnomad_genomes_af": 0.00000666231,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9532440900802612,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.492,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9865,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.372,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001317034.1",
"gene_symbol": "DPM1",
"hgnc_id": 3005,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.806G>A",
"hgvs_p": "p.Arg269His"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000558899.2",
"gene_symbol": "ADNP-AS1",
"hgnc_id": 51227,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.149+3765C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital disorder of glycosylation type 1E,Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Congenital disorder of glycosylation type 1E|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}