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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: 10-119162358-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=119162358&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 119162358,
"ref": "AG",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000355697.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.233delC",
"hgvs_p": "p.Pro78fs",
"transcript": "NM_213649.2",
"protein_id": "NP_998814.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 337,
"cds_start": 233,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 1556,
"mane_select": "ENST00000355697.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.233delC",
"hgvs_p": "p.Pro78fs",
"transcript": "ENST00000355697.7",
"protein_id": "ENSP00000347924.2",
"transcript_support_level": 1,
"aa_start": 78,
"aa_end": null,
"aa_length": 337,
"cds_start": 233,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 1556,
"mane_select": "NM_213649.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.233delC",
"hgvs_p": "p.Pro78fs",
"transcript": "XM_005269525.6",
"protein_id": "XP_005269582.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 328,
"cds_start": 233,
"cds_end": null,
"cds_length": 987,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.233delC",
"hgvs_p": "p.Pro78fs",
"transcript": "XM_047424584.1",
"protein_id": "XP_047280540.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 314,
"cds_start": 233,
"cds_end": null,
"cds_length": 945,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 1039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "n.240delC",
"hgvs_p": null,
"transcript": "ENST00000461438.5",
"protein_id": null,
"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": 1029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "n.122delC",
"hgvs_p": null,
"transcript": "ENST00000462913.1",
"protein_id": null,
"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": 278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "n.209delC",
"hgvs_p": null,
"transcript": "ENST00000466218.5",
"protein_id": null,
"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": 764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "n.278delC",
"hgvs_p": null,
"transcript": "NR_110305.1",
"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": 1482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.-116delC",
"hgvs_p": null,
"transcript": "ENST00000369131.8",
"protein_id": "ENSP00000358127.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.-89delC",
"hgvs_p": null,
"transcript": "ENST00000419372.5",
"protein_id": "ENSP00000414193.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.-116delC",
"hgvs_p": null,
"transcript": "XM_005269526.3",
"protein_id": "XP_005269583.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 221,
"cds_start": -4,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.-116delC",
"hgvs_p": null,
"transcript": "XM_011539282.3",
"protein_id": "XP_011537584.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 221,
"cds_start": -4,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"hgvs_c": "c.-201delC",
"hgvs_p": null,
"transcript": "XM_047424585.1",
"protein_id": "XP_047280541.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 221,
"cds_start": -4,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SFXN4",
"gene_hgnc_id": 16088,
"dbsnp": "rs398124642",
"frequency_reference_population": 0.0000020522139,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205221,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -1.79,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000355697.7",
"gene_symbol": "SFXN4",
"hgnc_id": 16088,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.233delC",
"hgvs_p": "p.Pro78fs"
}
],
"clinvar_disease": "Growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}