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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: 17-10639482-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=10639482&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 10639482,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000583535.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null,
"transcript": "NM_002470.4",
"protein_id": "NP_002461.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1940,
"cds_start": -4,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6032,
"mane_select": "ENST00000583535.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null,
"transcript": "ENST00000583535.6",
"protein_id": "ENSP00000464317.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1940,
"cds_start": -4,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6032,
"mane_select": "NM_002470.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MYHAS",
"gene_hgnc_id": 50609,
"hgvs_c": "n.705+25605G>A",
"hgvs_p": null,
"transcript": "ENST00000579914.2",
"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": 1006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MYHAS",
"gene_hgnc_id": 50609,
"hgvs_c": "n.1041+25605G>A",
"hgvs_p": null,
"transcript": "ENST00000584139.2",
"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": 1460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null,
"transcript": "XM_011523870.4",
"protein_id": "XP_011522172.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1940,
"cds_start": -4,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null,
"transcript": "XM_011523871.3",
"protein_id": "XP_011522173.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1940,
"cds_start": -4,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null,
"transcript": "XM_047436127.1",
"protein_id": "XP_047292083.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1940,
"cds_start": -4,
"cds_end": null,
"cds_length": 5823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYH3",
"gene_hgnc_id": 7573,
"dbsnp": "rs188588330",
"frequency_reference_population": 0.0030823962,
"hom_count_reference_population": 10,
"allele_count_reference_population": 4975,
"gnomad_exomes_af": 0.00311194,
"gnomad_genomes_af": 0.00279869,
"gnomad_exomes_ac": 4549,
"gnomad_genomes_ac": 426,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.47999998927116394,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.004000000189989805,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.483,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000641242868764466,
"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": "ENST00000583535.6",
"gene_symbol": "MYH3",
"hgnc_id": 7573,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2926-8C>T",
"hgvs_p": null
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000584139.2",
"gene_symbol": "MYHAS",
"hgnc_id": 50609,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1041+25605G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Distal arthrogryposis type 2B1,Freeman-Sheldon syndrome,MYH3-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:2",
"phenotype_combined": "Freeman-Sheldon syndrome|not provided|Distal arthrogryposis type 2B1|MYH3-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}