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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: 1-156815825-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=156815825&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 156815825,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_003975.4",
"consequences": [
{
"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": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "NM_003975.4",
"protein_id": "NP_003966.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 389,
"cds_start": -4,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1644,
"mane_select": "ENST00000368199.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "ENST00000368199.8",
"protein_id": "ENSP00000357182.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 389,
"cds_start": -4,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1644,
"mane_select": "NM_003975.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "ENST00000392306.2",
"protein_id": "ENSP00000376123.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 399,
"cds_start": -4,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.69+181C>T",
"hgvs_p": null,
"transcript": "ENST00000368198.8",
"protein_id": "ENSP00000357181.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": -4,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "n.186G>A",
"hgvs_p": null,
"transcript": "ENST00000489021.6",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "n.-77G>A",
"hgvs_p": null,
"transcript": "ENST00000497019.7",
"protein_id": "ENSP00000436804.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"transcript": "NM_001007792.1",
"protein_id": "NP_001007793.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 760,
"cds_start": -4,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "c.-77G>A",
"hgvs_p": null,
"transcript": "ENST00000392302.7",
"protein_id": "ENSP00000376120.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 736,
"cds_start": -4,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "c.-217G>A",
"hgvs_p": null,
"transcript": "ENST00000674537.2",
"protein_id": "ENSP00000502725.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 736,
"cds_start": -4,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTRK1",
"gene_hgnc_id": 8031,
"hgvs_c": "n.-77G>A",
"hgvs_p": null,
"transcript": "ENST00000497019.7",
"protein_id": "ENSP00000436804.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "NM_001161441.2",
"protein_id": "NP_001154913.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 399,
"cds_start": -4,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "NM_001161444.2",
"protein_id": "NP_001154916.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 389,
"cds_start": -4,
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"cds_length": 1170,
"cdna_start": null,
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"cdna_length": 1431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.69+181C>T",
"hgvs_p": null,
"transcript": "NM_001161442.2",
"protein_id": "NP_001154914.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": -4,
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"cds_length": 1116,
"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.39+181C>T",
"hgvs_p": null,
"transcript": "NM_001161443.2",
"protein_id": "NP_001154915.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "n.175+181C>T",
"hgvs_p": null,
"transcript": "ENST00000495306.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.141+181C>T",
"hgvs_p": null,
"transcript": "XM_017002762.3",
"protein_id": "XP_016858251.1",
"transcript_support_level": null,
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},
{
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"strand": false,
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],
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"exon_count": 9,
"intron_rank": 2,
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"gene_symbol": "SH2D2A",
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"hgvs_c": "c.141+181C>T",
"hgvs_p": null,
"transcript": "XM_006711615.3",
"protein_id": "XP_006711678.1",
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.123+181C>T",
"hgvs_p": null,
"transcript": "XM_017002764.3",
"protein_id": "XP_016858253.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 385,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.69+181C>T",
"hgvs_p": null,
"transcript": "XM_017002765.2",
"protein_id": "XP_016858254.1",
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},
{
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],
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"gene_symbol": "SH2D2A",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.141+181C>T",
"hgvs_p": null,
"transcript": "XM_047433652.1",
"protein_id": "XP_047289608.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"hgvs_c": "c.69+181C>T",
"hgvs_p": null,
"transcript": "XM_047433655.1",
"protein_id": "XP_047289611.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 367,
"cds_start": -4,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SH2D2A",
"gene_hgnc_id": 10821,
"dbsnp": "rs1800601",
"frequency_reference_population": 0.6750606,
"hom_count_reference_population": 370132,
"allele_count_reference_population": 1089140,
"gnomad_exomes_af": 0.679206,
"gnomad_genomes_af": 0.635183,
"gnomad_exomes_ac": 992629,
"gnomad_genomes_ac": 96511,
"gnomad_exomes_homalt": 338909,
"gnomad_genomes_homalt": 31223,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.839,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_003975.4",
"gene_symbol": "SH2D2A",
"hgnc_id": 10821,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.123+181C>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000497019.7",
"gene_symbol": "NTRK1",
"hgnc_id": 8031,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "n.-77G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary insensitivity to pain with anhidrosis,X-linked lymphoproliferative disease due to SH2D1A deficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Hereditary insensitivity to pain with anhidrosis|X-linked lymphoproliferative disease due to SH2D1A deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}