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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: 6-130175981-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=130175981&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 130175981,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001277185.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "NM_001017373.4",
"protein_id": "NP_001017373.2",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000439090.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017373.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "ENST00000439090.7",
"protein_id": "ENSP00000403565.2",
"transcript_support_level": 2,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001017373.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439090.7"
},
{
"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": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "n.1359C>T",
"hgvs_p": null,
"transcript": "ENST00000533296.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000533296.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.754C>T",
"hgvs_p": "p.Arg252Cys",
"transcript": "NM_001277185.2",
"protein_id": "NP_001264114.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 544,
"cds_start": 754,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277185.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.754C>T",
"hgvs_p": "p.Arg252Cys",
"transcript": "ENST00000457563.6",
"protein_id": "ENSP00000402092.2",
"transcript_support_level": 2,
"aa_start": 252,
"aa_end": null,
"aa_length": 544,
"cds_start": 754,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457563.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "NM_001258275.3",
"protein_id": "NP_001245204.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001258275.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "ENST00000368134.6",
"protein_id": "ENSP00000357116.2",
"transcript_support_level": 2,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368134.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "ENST00000437477.6",
"protein_id": "ENSP00000391163.2",
"transcript_support_level": 5,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437477.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.676C>T",
"hgvs_p": "p.Arg226Cys",
"transcript": "ENST00000532763.5",
"protein_id": "ENSP00000436088.1",
"transcript_support_level": 5,
"aa_start": 226,
"aa_end": null,
"aa_length": 275,
"cds_start": 676,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000532763.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "XM_024446333.2",
"protein_id": "XP_024302101.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 540,
"cds_start": 742,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024446333.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.739C>T",
"hgvs_p": "p.Arg247Cys",
"transcript": "XM_017010305.2",
"protein_id": "XP_016865794.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 539,
"cds_start": 739,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010305.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "XM_024446335.2",
"protein_id": "XP_024302103.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024446335.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "XM_024446337.2",
"protein_id": "XP_024302105.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024446337.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Arg228Cys",
"transcript": "XM_047418239.1",
"protein_id": "XP_047274195.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 520,
"cds_start": 682,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418239.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "XM_017010308.3",
"protein_id": "XP_016865797.2",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 374,
"cds_start": 742,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010308.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "c.*60C>T",
"hgvs_p": null,
"transcript": "XM_017010309.3",
"protein_id": "XP_016865798.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 258,
"cds_start": null,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010309.3"
},
{
"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": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "n.308C>T",
"hgvs_p": null,
"transcript": "ENST00000526886.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000526886.5"
},
{
"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": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "n.335C>T",
"hgvs_p": null,
"transcript": "ENST00000528422.5",
"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": "ENST00000528422.5"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"hgvs_c": "n.869C>T",
"hgvs_p": null,
"transcript": "XR_001743174.3",
"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": "XR_001743174.3"
}
],
"gene_symbol": "SAMD3",
"gene_hgnc_id": 21574,
"dbsnp": "rs201988282",
"frequency_reference_population": 0.00003535366,
"hom_count_reference_population": 0,
"allele_count_reference_population": 57,
"gnomad_exomes_af": 0.0000342427,
"gnomad_genomes_af": 0.0000460175,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7857632040977478,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.311,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7609,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.847,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001277185.2",
"gene_symbol": "SAMD3",
"hgnc_id": 21574,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.754C>T",
"hgvs_p": "p.Arg252Cys"
}
],
"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
}