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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: 1-53796907-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53796907&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53796907,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018087.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu",
"transcript": "NM_018087.5",
"protein_id": "NP_060557.3",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 674,
"cds_start": 1460,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 1495,
"cdna_end": null,
"cdna_length": 4552,
"mane_select": "ENST00000371429.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018087.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu",
"transcript": "ENST00000371429.4",
"protein_id": "ENSP00000360483.3",
"transcript_support_level": 1,
"aa_start": 487,
"aa_end": null,
"aa_length": 674,
"cds_start": 1460,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 1495,
"cdna_end": null,
"cdna_length": 4552,
"mane_select": "NM_018087.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371429.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1481C>T",
"hgvs_p": "p.Ser494Leu",
"transcript": "ENST00000923529.1",
"protein_id": "ENSP00000593588.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 681,
"cds_start": 1481,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 4599,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923529.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1457C>T",
"hgvs_p": "p.Ser486Leu",
"transcript": "ENST00000874541.1",
"protein_id": "ENSP00000544600.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 673,
"cds_start": 1457,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 1753,
"cdna_end": null,
"cdna_length": 4815,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874541.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu",
"transcript": "ENST00000874543.1",
"protein_id": "ENSP00000544602.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 669,
"cds_start": 1460,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1502,
"cdna_end": null,
"cdna_length": 4544,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874543.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1436C>T",
"hgvs_p": "p.Ser479Leu",
"transcript": "ENST00000874547.1",
"protein_id": "ENSP00000544606.1",
"transcript_support_level": null,
"aa_start": 479,
"aa_end": null,
"aa_length": 666,
"cds_start": 1436,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 1457,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874547.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu",
"transcript": "ENST00000874542.1",
"protein_id": "ENSP00000544601.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 657,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1974,
"cdna_start": 1759,
"cdna_end": null,
"cdna_length": 4765,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874542.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1367C>T",
"hgvs_p": "p.Ser456Leu",
"transcript": "ENST00000874548.1",
"protein_id": "ENSP00000544607.1",
"transcript_support_level": null,
"aa_start": 456,
"aa_end": null,
"aa_length": 643,
"cds_start": 1367,
"cds_end": null,
"cds_length": 1932,
"cdna_start": 1405,
"cdna_end": null,
"cdna_length": 2218,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874548.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Ser453Leu",
"transcript": "ENST00000874546.1",
"protein_id": "ENSP00000544605.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 640,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1379,
"cdna_end": null,
"cdna_length": 4436,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874546.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1349C>T",
"hgvs_p": "p.Ser450Leu",
"transcript": "ENST00000923528.1",
"protein_id": "ENSP00000593587.1",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 637,
"cds_start": 1349,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1563,
"cdna_end": null,
"cdna_length": 4620,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923528.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1340C>T",
"hgvs_p": "p.Ser447Leu",
"transcript": "NM_001168551.2",
"protein_id": "NP_001162023.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 634,
"cds_start": 1340,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 1375,
"cdna_end": null,
"cdna_length": 4432,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001168551.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1340C>T",
"hgvs_p": "p.Ser447Leu",
"transcript": "ENST00000923530.1",
"protein_id": "ENSP00000593589.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 634,
"cds_start": 1340,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 1380,
"cdna_end": null,
"cdna_length": 4437,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923530.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Ser435Leu",
"transcript": "ENST00000874545.1",
"protein_id": "ENSP00000544604.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 622,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1869,
"cdna_start": 1339,
"cdna_end": null,
"cdna_length": 4389,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874545.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu",
"transcript": "ENST00000874544.1",
"protein_id": "ENSP00000544603.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 619,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1500,
"cdna_end": null,
"cdna_length": 4392,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874544.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Ser314Leu",
"transcript": "ENST00000923527.1",
"protein_id": "ENSP00000593586.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 501,
"cds_start": 941,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 1161,
"cdna_end": null,
"cdna_length": 4223,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923527.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1457C>T",
"hgvs_p": "p.Ser486Leu",
"transcript": "XM_011541766.3",
"protein_id": "XP_011540068.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 673,
"cds_start": 1457,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 1632,
"cdna_end": null,
"cdna_length": 4689,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541766.3"
},
{
"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": 17,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1223-103C>T",
"hgvs_p": null,
"transcript": "ENST00000923531.1",
"protein_id": "ENSP00000593590.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 592,
"cds_start": null,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2299,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923531.1"
},
{
"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": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.1222+3786C>T",
"hgvs_p": null,
"transcript": "ENST00000923526.1",
"protein_id": "ENSP00000593585.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 515,
"cds_start": null,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4299,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923526.1"
},
{
"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": 14,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.985-3628C>T",
"hgvs_p": null,
"transcript": "ENST00000945040.1",
"protein_id": "ENSP00000615099.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": null,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1719,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945040.1"
},
{
"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": 13,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "c.892-3628C>T",
"hgvs_p": null,
"transcript": "ENST00000945039.1",
"protein_id": "ENSP00000615098.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 443,
"cds_start": null,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3892,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945039.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"hgvs_c": "n.1374C>T",
"hgvs_p": null,
"transcript": "NR_033142.2",
"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": 4431,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033142.2"
}
],
"gene_symbol": "NDC1",
"gene_hgnc_id": 25525,
"dbsnp": "rs777722453",
"frequency_reference_population": 0.000003718071,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000273684,
"gnomad_genomes_af": 0.0000131404,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1594526767730713,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20000000298023224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.1084,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.783,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.2,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018087.5",
"gene_symbol": "NDC1",
"hgnc_id": 25525,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Ser487Leu"
}
],
"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
}