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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: 1-21577638-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21577638&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21577638,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000374840.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "NM_000478.6",
"protein_id": "NP_000469.3",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1764,
"cdna_end": null,
"cdna_length": 2536,
"mane_select": "ENST00000374840.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "ENST00000374840.8",
"protein_id": "ENSP00000363973.3",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1764,
"cdna_end": null,
"cdna_length": 2536,
"mane_select": "NM_000478.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "NM_001369803.2",
"protein_id": "NP_001356732.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1828,
"cdna_end": null,
"cdna_length": 2600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "NM_001369804.2",
"protein_id": "NP_001356733.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1762,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "NM_001369805.2",
"protein_id": "NP_001356734.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1797,
"cdna_end": null,
"cdna_length": 2569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala",
"transcript": "ENST00000374832.5",
"protein_id": "ENSP00000363965.1",
"transcript_support_level": 2,
"aa_start": 522,
"aa_end": null,
"aa_length": 524,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1819,
"cdna_end": null,
"cdna_length": 2193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1400T>C",
"hgvs_p": "p.Val467Ala",
"transcript": "NM_001127501.4",
"protein_id": "NP_001120973.2",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 469,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1599,
"cdna_end": null,
"cdna_length": 2371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1400T>C",
"hgvs_p": "p.Val467Ala",
"transcript": "ENST00000540617.5",
"protein_id": "ENSP00000442672.1",
"transcript_support_level": 2,
"aa_start": 467,
"aa_end": null,
"aa_length": 469,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1594,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1334T>C",
"hgvs_p": "p.Val445Ala",
"transcript": "NM_001177520.3",
"protein_id": "NP_001170991.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 447,
"cds_start": 1334,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 2255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1334T>C",
"hgvs_p": "p.Val445Ala",
"transcript": "ENST00000539907.5",
"protein_id": "ENSP00000437674.1",
"transcript_support_level": 2,
"aa_start": 445,
"aa_end": null,
"aa_length": 447,
"cds_start": 1334,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 2241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.638T>C",
"hgvs_p": "p.Val213Ala",
"transcript": "ENST00000374830.2",
"protein_id": "ENSP00000363963.2",
"transcript_support_level": 4,
"aa_start": 213,
"aa_end": null,
"aa_length": 215,
"cds_start": 638,
"cds_end": null,
"cds_length": 648,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "c.1409T>C",
"hgvs_p": "p.Val470Ala",
"transcript": "XM_017000903.2",
"protein_id": "XP_016856392.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 472,
"cds_start": 1409,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1409,
"cdna_end": null,
"cdna_length": 2181,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"hgvs_c": "n.834T>C",
"hgvs_p": null,
"transcript": "ENST00000374829.2",
"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": 1595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALPL",
"gene_hgnc_id": 438,
"dbsnp": "rs34605986",
"frequency_reference_population": 0.10660742,
"hom_count_reference_population": 9914,
"allele_count_reference_population": 170290,
"gnomad_exomes_af": 0.109364,
"gnomad_genomes_af": 0.0804411,
"gnomad_exomes_ac": 158043,
"gnomad_genomes_ac": 12247,
"gnomad_exomes_homalt": 9320,
"gnomad_genomes_homalt": 594,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0013977885246276855,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.257,
"revel_prediction": "Benign",
"alphamissense_score": 0.0774,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.497,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000374840.8",
"gene_symbol": "ALPL",
"hgnc_id": 438,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1565T>C",
"hgvs_p": "p.Val522Ala"
}
],
"clinvar_disease": "Adult hypophosphatasia,Childhood hypophosphatasia,Hypophosphatasia,Infantile hypophosphatasia,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:11 O:1",
"phenotype_combined": "not specified|Hypophosphatasia|Infantile hypophosphatasia|Childhood hypophosphatasia|Adult hypophosphatasia|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}