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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: 11-62801631-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=62801631&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 62801631,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000294172.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "NM_006362.5",
"protein_id": "NP_006353.2",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 619,
"cds_start": 640,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "ENST00000294172.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "ENST00000294172.7",
"protein_id": "ENSP00000294172.2",
"transcript_support_level": 1,
"aa_start": 214,
"aa_end": null,
"aa_length": 619,
"cds_start": 640,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "NM_006362.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.769C>G",
"hgvs_p": "p.Leu257Val",
"transcript": "ENST00000530875.5",
"protein_id": "ENSP00000435742.1",
"transcript_support_level": 1,
"aa_start": 257,
"aa_end": null,
"aa_length": 602,
"cds_start": 769,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "ENST00000531709.6",
"protein_id": "ENSP00000453885.1",
"transcript_support_level": 1,
"aa_start": 214,
"aa_end": null,
"aa_length": 356,
"cds_start": 640,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 754,
"cdna_end": null,
"cdna_length": 4128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "ENST00000532297.5",
"protein_id": "ENSP00000436679.1",
"transcript_support_level": 5,
"aa_start": 214,
"aa_end": null,
"aa_length": 619,
"cds_start": 640,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 2795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "NM_001081491.2",
"protein_id": "NP_001074960.1",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 356,
"cds_start": 640,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.229C>G",
"hgvs_p": "p.Leu77Val",
"transcript": "ENST00000531131.1",
"protein_id": "ENSP00000477375.1",
"transcript_support_level": 2,
"aa_start": 77,
"aa_end": null,
"aa_length": 219,
"cds_start": 229,
"cds_end": null,
"cds_length": 660,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 1023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.688C>G",
"hgvs_p": "p.Leu230Val",
"transcript": "XM_047426245.1",
"protein_id": "XP_047282201.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 635,
"cds_start": 688,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.688C>G",
"hgvs_p": "p.Leu230Val",
"transcript": "XM_047426246.1",
"protein_id": "XP_047282202.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 621,
"cds_start": 688,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 1620,
"cdna_end": null,
"cdna_length": 3144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val",
"transcript": "XM_047426247.1",
"protein_id": "XP_047282203.1",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 605,
"cds_start": 640,
"cds_end": null,
"cds_length": 1818,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 2248,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "n.157+2303C>G",
"hgvs_p": null,
"transcript": "ENST00000526163.5",
"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": 569,
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"hgvs_c": "n.226-214C>G",
"hgvs_p": null,
"transcript": "ENST00000531579.5",
"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": 590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NXF1",
"gene_hgnc_id": 8071,
"dbsnp": "rs191516295",
"frequency_reference_population": 0.0065214825,
"hom_count_reference_population": 47,
"allele_count_reference_population": 10505,
"gnomad_exomes_af": 0.00679053,
"gnomad_genomes_af": 0.00389791,
"gnomad_exomes_ac": 9921,
"gnomad_genomes_ac": 584,
"gnomad_exomes_homalt": 44,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007778912782669067,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.0860000029206276,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.12,
"revel_prediction": "Benign",
"alphamissense_score": 0.0931,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000521848408047728,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000294172.7",
"gene_symbol": "NXF1",
"hgnc_id": 8071,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Leu214Val"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}