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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: 5-74720648-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=74720648&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 74720648,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000261416.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1514G>A",
"hgvs_p": "p.Arg505Gln",
"transcript": "NM_000521.4",
"protein_id": "NP_000512.2",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 556,
"cds_start": 1514,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1542,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "ENST00000261416.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1514G>A",
"hgvs_p": "p.Arg505Gln",
"transcript": "ENST00000261416.12",
"protein_id": "ENSP00000261416.7",
"transcript_support_level": 1,
"aa_start": 505,
"aa_end": null,
"aa_length": 556,
"cds_start": 1514,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1542,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "NM_000521.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280Gln",
"transcript": "ENST00000511181.5",
"protein_id": "ENSP00000426285.1",
"transcript_support_level": 1,
"aa_start": 280,
"aa_end": null,
"aa_length": 331,
"cds_start": 839,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1751,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280Gln",
"transcript": "NM_001292004.2",
"protein_id": "NP_001278933.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 331,
"cds_start": 839,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1751,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.449G>A",
"hgvs_p": "p.Arg150Gln",
"transcript": "ENST00000513336.5",
"protein_id": "ENSP00000423713.1",
"transcript_support_level": 3,
"aa_start": 150,
"aa_end": null,
"aa_length": 201,
"cds_start": 449,
"cds_end": null,
"cds_length": 606,
"cdna_start": 450,
"cdna_end": null,
"cdna_length": 720,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.389G>A",
"hgvs_p": null,
"transcript": "ENST00000503312.5",
"protein_id": "ENSP00000426384.1",
"transcript_support_level": 5,
"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": 756,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.711G>A",
"hgvs_p": null,
"transcript": "ENST00000504459.5",
"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": 899,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.35G>A",
"hgvs_p": null,
"transcript": "ENST00000505859.1",
"protein_id": "ENSP00000424550.1",
"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": 604,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.233G>A",
"hgvs_p": null,
"transcript": "ENST00000513539.1",
"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": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.-50G>A",
"hgvs_p": null,
"transcript": "ENST00000509579.1",
"protein_id": "ENSP00000424939.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 35,
"cds_start": -4,
"cds_end": null,
"cds_length": 108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"dbsnp": "rs121907983",
"frequency_reference_population": 0.000043375345,
"hom_count_reference_population": 0,
"allele_count_reference_population": 70,
"gnomad_exomes_af": 0.0000465209,
"gnomad_genomes_af": 0.0000131484,
"gnomad_exomes_ac": 68,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9911832809448242,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.951,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6269,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.892,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000261416.12",
"gene_symbol": "HEXB",
"hgnc_id": 4879,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1514G>A",
"hgvs_p": "p.Arg505Gln"
}
],
"clinvar_disease": " adult form,Sandhoff disease",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Sandhoff disease, adult form|Sandhoff disease",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}