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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: 12-51790425-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=51790425&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 51790425,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000354534.11",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys",
"transcript": "NM_001330260.2",
"protein_id": "NP_001317189.1",
"transcript_support_level": null,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1980,
"cds_start": 4447,
"cds_end": null,
"cds_length": 5943,
"cdna_start": 4628,
"cdna_end": null,
"cdna_length": 11559,
"mane_select": "ENST00000627620.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys",
"transcript": "NM_014191.4",
"protein_id": "NP_055006.1",
"transcript_support_level": null,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1980,
"cds_start": 4447,
"cds_end": null,
"cds_length": 5943,
"cdna_start": 4628,
"cdna_end": null,
"cdna_length": 11559,
"mane_select": null,
"mane_plus": "ENST00000354534.11",
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys",
"transcript": "ENST00000354534.11",
"protein_id": "ENSP00000346534.4",
"transcript_support_level": 1,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1980,
"cds_start": 4447,
"cds_end": null,
"cds_length": 5943,
"cdna_start": 4628,
"cdna_end": null,
"cdna_length": 11559,
"mane_select": null,
"mane_plus": "NM_014191.4",
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys",
"transcript": "ENST00000627620.5",
"protein_id": "ENSP00000487583.2",
"transcript_support_level": 5,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1980,
"cds_start": 4447,
"cds_end": null,
"cds_length": 5943,
"cdna_start": 4628,
"cdna_end": null,
"cdna_length": 11559,
"mane_select": "NM_001330260.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4480G>A",
"hgvs_p": "p.Glu1494Lys",
"transcript": "ENST00000599343.5",
"protein_id": "ENSP00000476447.3",
"transcript_support_level": 5,
"aa_start": 1494,
"aa_end": null,
"aa_length": 1991,
"cds_start": 4480,
"cds_end": null,
"cds_length": 5976,
"cdna_start": 4480,
"cdna_end": null,
"cdna_length": 5976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Glu1442Lys",
"transcript": "ENST00000355133.7",
"protein_id": "ENSP00000347255.4",
"transcript_support_level": 1,
"aa_start": 1442,
"aa_end": null,
"aa_length": 1939,
"cds_start": 4324,
"cds_end": null,
"cds_length": 5820,
"cdna_start": 4324,
"cdna_end": null,
"cdna_length": 5820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys",
"transcript": "ENST00000662684.1",
"protein_id": "ENSP00000499636.1",
"transcript_support_level": null,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1980,
"cds_start": 4447,
"cds_end": null,
"cds_length": 5943,
"cdna_start": 4595,
"cdna_end": null,
"cdna_length": 6930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Glu1442Lys",
"transcript": "NM_001177984.3",
"protein_id": "NP_001171455.1",
"transcript_support_level": null,
"aa_start": 1442,
"aa_end": null,
"aa_length": 1939,
"cds_start": 4324,
"cds_end": null,
"cds_length": 5820,
"cdna_start": 4505,
"cdna_end": null,
"cdna_length": 11436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Glu1442Lys",
"transcript": "NM_001369788.1",
"protein_id": "NP_001356717.1",
"transcript_support_level": null,
"aa_start": 1442,
"aa_end": null,
"aa_length": 1939,
"cds_start": 4324,
"cds_end": null,
"cds_length": 5820,
"cdna_start": 4505,
"cdna_end": null,
"cdna_length": 11436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Glu1442Lys",
"transcript": "ENST00000545061.5",
"protein_id": "ENSP00000440360.1",
"transcript_support_level": 5,
"aa_start": 1442,
"aa_end": null,
"aa_length": 1939,
"cds_start": 4324,
"cds_end": null,
"cds_length": 5820,
"cdna_start": 4502,
"cdna_end": null,
"cdna_length": 11433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Glu1442Lys",
"transcript": "ENST00000668547.1",
"protein_id": "ENSP00000499691.1",
"transcript_support_level": null,
"aa_start": 1442,
"aa_end": null,
"aa_length": 1939,
"cds_start": 4324,
"cds_end": null,
"cds_length": 5820,
"cdna_start": 4505,
"cdna_end": null,
"cdna_length": 6876,
"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": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "n.*1549G>A",
"hgvs_p": null,
"transcript": "ENST00000636945.2",
"protein_id": "ENSP00000490580.1",
"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": 3578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"hgvs_c": "n.*1549G>A",
"hgvs_p": null,
"transcript": "ENST00000636945.2",
"protein_id": "ENSP00000490580.1",
"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": 3578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN8A",
"gene_hgnc_id": 10596,
"dbsnp": "rs879255652",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9118932485580444,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.895,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9465,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000354534.11",
"gene_symbol": "SCN8A",
"hgnc_id": 10596,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4447G>A",
"hgvs_p": "p.Glu1483Lys"
}
],
"clinvar_disease": " 13, 5, benign familial infantile,Complex neurodevelopmental disorder,Developmental and epileptic encephalopathy,Epilepsy,Seizure,Seizures,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 O:1",
"phenotype_combined": "Seizures, benign familial infantile, 5|Epilepsy|Developmental and epileptic encephalopathy, 13|not provided|Seizure|Developmental and epileptic encephalopathy|Complex neurodevelopmental disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}