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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: 1-150510879-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=150510879&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 150510879,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000369047.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.389C>T",
"hgvs_p": "p.Thr130Met",
"transcript": "NM_004425.4",
"protein_id": "NP_004416.2",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 540,
"cds_start": 389,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 2046,
"mane_select": "ENST00000369047.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.389C>T",
"hgvs_p": "p.Thr130Met",
"transcript": "ENST00000369047.9",
"protein_id": "ENSP00000358043.4",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 540,
"cds_start": 389,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 2046,
"mane_select": "NM_004425.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.389C>T",
"hgvs_p": "p.Thr130Met",
"transcript": "ENST00000346569.6",
"protein_id": "ENSP00000271630.6",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 415,
"cds_start": 389,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 492,
"cdna_end": null,
"cdna_length": 1444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Thr157Met",
"transcript": "NM_001202858.2",
"protein_id": "NP_001189787.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 567,
"cds_start": 470,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 571,
"cdna_end": null,
"cdna_length": 2127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Thr157Met",
"transcript": "ENST00000369049.8",
"protein_id": "ENSP00000358045.4",
"transcript_support_level": 2,
"aa_start": 157,
"aa_end": null,
"aa_length": 567,
"cds_start": 470,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 1925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "c.389C>T",
"hgvs_p": "p.Thr130Met",
"transcript": "NM_022664.3",
"protein_id": "NP_073155.2",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 415,
"cds_start": 389,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 1671,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "n.1488C>T",
"hgvs_p": null,
"transcript": "ENST00000470432.5",
"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": 3066,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"hgvs_c": "n.676C>T",
"hgvs_p": null,
"transcript": "ENST00000498579.5",
"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": 943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307101",
"gene_hgnc_id": null,
"hgvs_c": "n.286-264G>A",
"hgvs_p": null,
"transcript": "ENST00000823869.1",
"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": 695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307101",
"gene_hgnc_id": null,
"hgvs_c": "n.305-525G>A",
"hgvs_p": null,
"transcript": "ENST00000823870.1",
"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": 816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307101",
"gene_hgnc_id": null,
"hgvs_c": "n.120-525G>A",
"hgvs_p": null,
"transcript": "ENST00000823872.1",
"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": 431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ECM1",
"gene_hgnc_id": 3153,
"dbsnp": "rs3737240",
"frequency_reference_population": 0.3718505,
"hom_count_reference_population": 117482,
"allele_count_reference_population": 599867,
"gnomad_exomes_af": 0.379611,
"gnomad_genomes_af": 0.297302,
"gnomad_exomes_ac": 554645,
"gnomad_genomes_ac": 45222,
"gnomad_exomes_homalt": 109298,
"gnomad_genomes_homalt": 8184,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00096169114112854,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.154,
"revel_prediction": "Benign",
"alphamissense_score": 0.0702,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.398,
"phylop100way_prediction": "Benign",
"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": -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": "ENST00000369047.9",
"gene_symbol": "ECM1",
"hgnc_id": 3153,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.389C>T",
"hgvs_p": "p.Thr130Met"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000823869.1",
"gene_symbol": "ENSG00000307101",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.286-264G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Lipid proteinosis,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided|Lipid proteinosis",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}