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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: 1-21568246-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21568246&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21568246,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000374840.8",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "NM_000478.6",
"protein_id": "NP_000469.3",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 990,
"cdna_end": null,
"cdna_length": 2536,
"mane_select": "ENST00000374840.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "ENST00000374840.8",
"protein_id": "ENSP00000363973.3",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 990,
"cdna_end": null,
"cdna_length": 2536,
"mane_select": "NM_000478.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "NM_001369803.2",
"protein_id": "NP_001356732.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 2600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "NM_001369804.2",
"protein_id": "NP_001356733.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 988,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "NM_001369805.2",
"protein_id": "NP_001356734.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 2569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg",
"transcript": "ENST00000374832.5",
"protein_id": "ENSP00000363965.1",
"transcript_support_level": 2,
"aa_start": 264,
"aa_end": null,
"aa_length": 524,
"cds_start": 791,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 2193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.626A>G",
"hgvs_p": "p.Lys209Arg",
"transcript": "NM_001127501.4",
"protein_id": "NP_001120973.2",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 469,
"cds_start": 626,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 2371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.626A>G",
"hgvs_p": "p.Lys209Arg",
"transcript": "ENST00000540617.5",
"protein_id": "ENSP00000442672.1",
"transcript_support_level": 2,
"aa_start": 209,
"aa_end": null,
"aa_length": 469,
"cds_start": 626,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 820,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.560A>G",
"hgvs_p": "p.Lys187Arg",
"transcript": "NM_001177520.3",
"protein_id": "NP_001170991.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 447,
"cds_start": 560,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 2255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.560A>G",
"hgvs_p": "p.Lys187Arg",
"transcript": "ENST00000539907.5",
"protein_id": "ENSP00000437674.1",
"transcript_support_level": 2,
"aa_start": 187,
"aa_end": null,
"aa_length": 447,
"cds_start": 560,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 706,
"cdna_end": null,
"cdna_length": 2241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Lys212Arg",
"transcript": "XM_017000903.2",
"protein_id": "XP_016856392.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 472,
"cds_start": 635,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 635,
"cdna_end": null,
"cdna_length": 2181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"dbsnp": "rs786204442",
"frequency_reference_population": 0.0000037176333,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000273629,
"gnomad_genomes_af": 0.0000131494,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4288392961025238,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9900000095367432,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.502,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0744,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.688,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.32,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999009126821569,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000374840.8",
"gene_symbol": "ALPL",
"hgnc_id": 438,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.791A>G",
"hgvs_p": "p.Lys264Arg"
}
],
"clinvar_disease": "Adult hypophosphatasia,Childhood hypophosphatasia,Hypophosphatasia,Infantile hypophosphatasia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3",
"phenotype_combined": "Infantile hypophosphatasia|not provided|Hypophosphatasia|Adult hypophosphatasia;Childhood hypophosphatasia;Infantile hypophosphatasia|Adult hypophosphatasia",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}