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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: 3-197996244-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=197996244&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 197996244,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000420910.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1093G>T",
"hgvs_p": "p.Gly365Cys",
"transcript": "NM_001136049.3",
"protein_id": "NP_001129521.3",
"transcript_support_level": null,
"aa_start": 365,
"aa_end": null,
"aa_length": 684,
"cds_start": 1093,
"cds_end": null,
"cds_length": 2055,
"cdna_start": 1122,
"cdna_end": null,
"cdna_length": 7137,
"mane_select": "ENST00000420910.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1093G>T",
"hgvs_p": "p.Gly365Cys",
"transcript": "ENST00000420910.7",
"protein_id": "ENSP00000410926.3",
"transcript_support_level": 1,
"aa_start": 365,
"aa_end": null,
"aa_length": 684,
"cds_start": 1093,
"cds_end": null,
"cds_length": 2055,
"cdna_start": 1122,
"cdna_end": null,
"cdna_length": 7137,
"mane_select": "NM_001136049.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1093G>T",
"hgvs_p": "p.Gly365Cys",
"transcript": "ENST00000330198.8",
"protein_id": "ENSP00000328829.5",
"transcript_support_level": 1,
"aa_start": 365,
"aa_end": null,
"aa_length": 647,
"cds_start": 1093,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 7043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.397G>T",
"hgvs_p": "p.Gly133Cys",
"transcript": "ENST00000482695.5",
"protein_id": "ENSP00000418324.2",
"transcript_support_level": 1,
"aa_start": 133,
"aa_end": null,
"aa_length": 452,
"cds_start": 397,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1018,
"cdna_end": null,
"cdna_length": 2010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.397G>T",
"hgvs_p": "p.Gly133Cys",
"transcript": "ENST00000332636.5",
"protein_id": "ENSP00000328611.6",
"transcript_support_level": 1,
"aa_start": 133,
"aa_end": null,
"aa_length": 415,
"cds_start": 397,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1093G>T",
"hgvs_p": "p.Gly365Cys",
"transcript": "NM_033029.4",
"protein_id": "NP_149018.3",
"transcript_support_level": null,
"aa_start": 365,
"aa_end": null,
"aa_length": 647,
"cds_start": 1093,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1122,
"cdna_end": null,
"cdna_length": 7026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1102G>T",
"hgvs_p": "p.Gly368Cys",
"transcript": "XM_047449155.1",
"protein_id": "XP_047305111.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 687,
"cds_start": 1102,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 7122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "c.1102G>T",
"hgvs_p": "p.Gly368Cys",
"transcript": "XM_047449156.1",
"protein_id": "XP_047305112.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 650,
"cds_start": 1102,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 7011,
"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": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.1608G>T",
"hgvs_p": null,
"transcript": "ENST00000451139.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 5998,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.428G>T",
"hgvs_p": null,
"transcript": "ENST00000472063.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 724,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.575G>T",
"hgvs_p": null,
"transcript": "ENST00000473676.5",
"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": 644,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.319G>T",
"hgvs_p": null,
"transcript": "ENST00000476356.5",
"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": 567,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.133G>T",
"hgvs_p": null,
"transcript": "ENST00000480813.1",
"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": 648,
"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": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.1001G>T",
"hgvs_p": null,
"transcript": "NR_026786.2",
"protein_id": null,
"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": 7016,
"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": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.1001G>T",
"hgvs_p": null,
"transcript": "NR_026787.2",
"protein_id": null,
"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": 6905,
"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": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"hgvs_c": "n.1122G>T",
"hgvs_p": null,
"transcript": "XR_007095764.1",
"protein_id": null,
"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": 6611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LMLN",
"gene_hgnc_id": 15991,
"dbsnp": "rs193920933",
"frequency_reference_population": 6.8842644e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.88426e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9821470379829407,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.823,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9678,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.504,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": "ENST00000420910.7",
"gene_symbol": "LMLN",
"hgnc_id": 15991,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1093G>T",
"hgvs_p": "p.Gly365Cys"
}
],
"clinvar_disease": "Prostate cancer",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Prostate cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}