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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: 7-48007194-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=48007194&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 48007194,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152782.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "NM_001030019.2",
"protein_id": "NP_001025190.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 357,
"cds_start": 463,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000297325.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001030019.2"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "ENST00000297325.9",
"protein_id": "ENSP00000297325.4",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 357,
"cds_start": 463,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001030019.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000297325.9"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "ENST00000395572.6",
"protein_id": "ENSP00000378939.2",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 357,
"cds_start": 463,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395572.6"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.163G>T",
"hgvs_p": "p.Asp55Tyr",
"transcript": "ENST00000438771.5",
"protein_id": "ENSP00000409077.1",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 269,
"cds_start": 163,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000438771.5"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "NM_152782.4",
"protein_id": "NP_689995.3",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 357,
"cds_start": 463,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152782.4"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.427G>T",
"hgvs_p": "p.Asp143Tyr",
"transcript": "NM_001284350.2",
"protein_id": "NP_001271279.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 345,
"cds_start": 427,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284350.2"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.427G>T",
"hgvs_p": "p.Asp143Tyr",
"transcript": "ENST00000412142.5",
"protein_id": "ENSP00000410204.2",
"transcript_support_level": 5,
"aa_start": 143,
"aa_end": null,
"aa_length": 345,
"cds_start": 427,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412142.5"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.220G>T",
"hgvs_p": "p.Asp74Tyr",
"transcript": "ENST00000453071.5",
"protein_id": "ENSP00000388627.1",
"transcript_support_level": 5,
"aa_start": 74,
"aa_end": null,
"aa_length": 280,
"cds_start": 220,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000453071.5"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "XM_047420113.1",
"protein_id": "XP_047276069.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 360,
"cds_start": 463,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420113.1"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "XM_047420114.1",
"protein_id": "XP_047276070.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 360,
"cds_start": 463,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420114.1"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr",
"transcript": "XM_017011930.2",
"protein_id": "XP_016867419.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 357,
"cds_start": 463,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011930.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "n.*291G>T",
"hgvs_p": null,
"transcript": "ENST00000449896.2",
"protein_id": "ENSP00000395392.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000449896.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"hgvs_c": "n.*291G>T",
"hgvs_p": null,
"transcript": "ENST00000449896.2",
"protein_id": "ENSP00000395392.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000449896.2"
}
],
"gene_symbol": "SUN3",
"gene_hgnc_id": 22429,
"dbsnp": "rs765732753",
"frequency_reference_population": 0.00002977442,
"hom_count_reference_population": 0,
"allele_count_reference_population": 48,
"gnomad_exomes_af": 0.0000321919,
"gnomad_genomes_af": 0.0000065735,
"gnomad_exomes_ac": 47,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05944603681564331,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.11,
"revel_prediction": "Benign",
"alphamissense_score": 0.0768,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.411,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_152782.4",
"gene_symbol": "SUN3",
"hgnc_id": 22429,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.463G>T",
"hgvs_p": "p.Asp155Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}