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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: 1-32275991-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=32275991&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 32275991,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000336890.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "NM_005356.5",
"protein_id": "NP_005347.3",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 509,
"cds_start": 559,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 671,
"cdna_end": null,
"cdna_length": 2091,
"mane_select": "ENST00000336890.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "ENST00000336890.10",
"protein_id": "ENSP00000337825.5",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 509,
"cds_start": 559,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 671,
"cdna_end": null,
"cdna_length": 2091,
"mane_select": "NM_005356.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "ENST00000333070.4",
"protein_id": "ENSP00000328213.4",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 539,
"cds_start": 559,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 2166,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.618G>A",
"hgvs_p": null,
"transcript": "ENST00000469765.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.733G>A",
"hgvs_p": "p.Asp245Asn",
"transcript": "NM_001439146.1",
"protein_id": "NP_001426075.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 567,
"cds_start": 733,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 2265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.733G>A",
"hgvs_p": "p.Asp245Asn",
"transcript": "ENST00000482949.6",
"protein_id": "ENSP00000431517.2",
"transcript_support_level": 5,
"aa_start": 245,
"aa_end": null,
"aa_length": 567,
"cds_start": 733,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 2257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "NM_001042771.3",
"protein_id": "NP_001036236.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 509,
"cds_start": 559,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 670,
"cdna_end": null,
"cdna_length": 2090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "NM_001330468.2",
"protein_id": "NP_001317397.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 458,
"cds_start": 559,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 671,
"cdna_end": null,
"cdna_length": 1938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "ENST00000495610.7",
"protein_id": "ENSP00000435605.2",
"transcript_support_level": 5,
"aa_start": 187,
"aa_end": null,
"aa_length": 458,
"cds_start": 559,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 680,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Asp231Asn",
"transcript": "ENST00000373557.6",
"protein_id": "ENSP00000362658.2",
"transcript_support_level": 3,
"aa_start": 231,
"aa_end": null,
"aa_length": 284,
"cds_start": 691,
"cds_end": null,
"cds_length": 855,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.733G>A",
"hgvs_p": "p.Asp245Asn",
"transcript": "XM_024447047.2",
"protein_id": "XP_024302815.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 567,
"cds_start": 733,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Asp231Asn",
"transcript": "XM_047420399.1",
"protein_id": "XP_047276355.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 553,
"cds_start": 691,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.733G>A",
"hgvs_p": "p.Asp245Asn",
"transcript": "XM_011541453.3",
"protein_id": "XP_011539755.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 516,
"cds_start": 733,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 2112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn",
"transcript": "XM_047420403.1",
"protein_id": "XP_047276359.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 458,
"cds_start": 559,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 670,
"cdna_end": null,
"cdna_length": 1937,
"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": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.1082G>A",
"hgvs_p": null,
"transcript": "ENST00000355928.8",
"protein_id": null,
"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": 2480,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.131G>A",
"hgvs_p": null,
"transcript": "ENST00000469956.1",
"protein_id": null,
"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": 923,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.*5G>A",
"hgvs_p": null,
"transcript": "ENST00000696991.1",
"protein_id": "ENSP00000513027.1",
"transcript_support_level": null,
"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": 1451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.*5G>A",
"hgvs_p": null,
"transcript": "ENST00000696991.1",
"protein_id": "ENSP00000513027.1",
"transcript_support_level": null,
"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": 1451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"hgvs_c": "n.*249G>A",
"hgvs_p": null,
"transcript": "ENST00000696990.1",
"protein_id": "ENSP00000513026.1",
"transcript_support_level": null,
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LCK",
"gene_hgnc_id": 6524,
"dbsnp": "rs539280346",
"frequency_reference_population": 0.000009292967,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000957676,
"gnomad_genomes_af": 0.00000656806,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8802183270454407,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.779,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9825,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.956,
"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": 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": "ENST00000336890.10",
"gene_symbol": "LCK",
"hgnc_id": 6524,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Asp187Asn"
}
],
"clinvar_disease": "Severe combined immunodeficiency due to LCK deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Severe combined immunodeficiency due to LCK deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}