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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: 7-892310-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=892310&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"stop_gained"
],
"gene_symbol": "GET4",
"hgnc_id": 21690,
"hgvs_c": "c.638C>A",
"hgvs_p": "p.Ser213*",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_015949.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SUN1",
"hgnc_id": 18587,
"hgvs_c": "n.*333C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000457861.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.28,
"chr": "7",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.2800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 327,
"aa_ref": "S",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2090,
"cdna_start": 730,
"cds_end": null,
"cds_length": 984,
"cds_start": 638,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_015949.3",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.638C>A",
"hgvs_p": "p.Ser213*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265857.8",
"protein_coding": true,
"protein_id": "NP_057033.2",
"strand": true,
"transcript": "NM_015949.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 327,
"aa_ref": "S",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2090,
"cdna_start": 730,
"cds_end": null,
"cds_length": 984,
"cds_start": 638,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000265857.8",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.638C>A",
"hgvs_p": "p.Ser213*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015949.3",
"protein_coding": true,
"protein_id": "ENSP00000265857.3",
"strand": true,
"transcript": "ENST00000265857.8",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 274,
"aa_ref": "S",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4356,
"cdna_start": 2996,
"cds_end": null,
"cds_length": 825,
"cds_start": 479,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000407192.5",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.479C>A",
"hgvs_p": "p.Ser160*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385646.1",
"strand": true,
"transcript": "ENST00000407192.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 333,
"aa_ref": "S",
"aa_start": 219,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1362,
"cdna_start": 749,
"cds_end": null,
"cds_length": 1002,
"cds_start": 656,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000919176.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.656C>A",
"hgvs_p": "p.Ser219*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589235.1",
"strand": true,
"transcript": "ENST00000919176.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 319,
"aa_ref": "S",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2028,
"cdna_start": 670,
"cds_end": null,
"cds_length": 960,
"cds_start": 614,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000881398.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.614C>A",
"hgvs_p": "p.Ser205*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551457.1",
"strand": true,
"transcript": "ENST00000881398.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 288,
"aa_ref": "S",
"aa_start": 174,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1154,
"cdna_start": 541,
"cds_end": null,
"cds_length": 867,
"cds_start": 521,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000954536.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.521C>A",
"hgvs_p": "p.Ser174*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624595.1",
"strand": true,
"transcript": "ENST00000954536.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 277,
"aa_ref": "S",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1262,
"cdna_start": 648,
"cds_end": null,
"cds_length": 834,
"cds_start": 488,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000919175.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.488C>A",
"hgvs_p": "p.Ser163*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589234.1",
"strand": true,
"transcript": "ENST00000919175.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 184,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 859,
"cdna_start": null,
"cds_end": null,
"cds_length": 555,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000954535.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.467-3024C>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624594.1",
"strand": true,
"transcript": "ENST00000954535.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 130,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1490,
"cdna_start": null,
"cds_end": null,
"cds_length": 393,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000919174.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "c.156-1430C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589233.1",
"strand": true,
"transcript": "ENST00000919174.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2975,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000457861.1",
"gene_hgnc_id": 18587,
"gene_symbol": "SUN1",
"hgvs_c": "n.*333C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000406444.1",
"strand": true,
"transcript": "ENST00000457861.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 676,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000464468.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "n.11C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000464468.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 370,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000483469.1",
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"hgvs_c": "n.206C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483469.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2975,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000457861.1",
"gene_hgnc_id": 18587,
"gene_symbol": "SUN1",
"hgvs_c": "n.*333C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000406444.1",
"strand": true,
"transcript": "ENST00000457861.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs747849277",
"effect": "stop_gained",
"frequency_reference_population": 6.943239e-7,
"gene_hgnc_id": 21690,
"gene_symbol": "GET4",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.94324e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.058,
"pos": 892310,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_015949.3"
}
]
}