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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: 12-51769127-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=51769127&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PP2",
"BP4",
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN8A",
"hgnc_id": 10596,
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"inheritance_mode": "AD,AR",
"pathogenic_score": 1,
"score": -1,
"transcript": "NM_014191.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4,BP6",
"acmg_score": -1,
"allele_count_reference_population": 54,
"alphamissense_prediction": null,
"alphamissense_score": 0.1281,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "12",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 13, 5, benign familial infantile,Cognitive impairment with or without cerebellar ataxia,Developmental and epileptic encephalopathy,Seizures,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.32182151079177856,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1980,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11559,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5943,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001330260.2",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000627620.5",
"protein_coding": true,
"protein_id": "NP_001317189.1",
"strand": true,
"transcript": "NM_001330260.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1980,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11559,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5943,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_014191.4",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "ENST00000354534.11",
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_055006.1",
"strand": true,
"transcript": "NM_014191.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1980,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11559,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5943,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000354534.11",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "NM_014191.4",
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000346534.4",
"strand": true,
"transcript": "ENST00000354534.11",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1980,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11559,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5943,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000627620.5",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001330260.2",
"protein_coding": true,
"protein_id": "ENSP00000487583.2",
"strand": true,
"transcript": "ENST00000627620.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1991,
"aa_ref": "R",
"aa_start": 1066,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5976,
"cdna_start": 3197,
"cds_end": null,
"cds_length": 5976,
"cds_start": 3197,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000599343.5",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3197G>A",
"hgvs_p": "p.Arg1066Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000476447.3",
"strand": true,
"transcript": "ENST00000599343.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5820,
"cdna_start": 3164,
"cds_end": null,
"cds_length": 5820,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000355133.7",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000347255.4",
"strand": true,
"transcript": "ENST00000355133.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1980,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6930,
"cdna_start": 3312,
"cds_end": null,
"cds_length": 5943,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000662684.1",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499636.1",
"strand": true,
"transcript": "ENST00000662684.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11436,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5820,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001177984.3",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171455.1",
"strand": true,
"transcript": "NM_001177984.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11436,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5820,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001369788.1",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001356717.1",
"strand": true,
"transcript": "NM_001369788.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11433,
"cdna_start": 3342,
"cds_end": null,
"cds_length": 5820,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000545061.5",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000440360.1",
"strand": true,
"transcript": "ENST00000545061.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "R",
"aa_start": 1055,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6876,
"cdna_start": 3345,
"cds_end": null,
"cds_length": 5820,
"cds_start": 3164,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000668547.1",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499691.1",
"strand": true,
"transcript": "ENST00000668547.1",
"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": 2075,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000548086.3",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "n.1010G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499511.1",
"strand": true,
"transcript": "ENST00000548086.3",
"transcript_support_level": 5
},
{
"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": 506,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000627665.1",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "n.156G>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": "ENST00000627665.1",
"transcript_support_level": 5
},
{
"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": 3578,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000636945.2",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "n.*266G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490580.1",
"strand": true,
"transcript": "ENST00000636945.2",
"transcript_support_level": 5
},
{
"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": 3578,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000636945.2",
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"hgvs_c": "n.*266G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490580.1",
"strand": true,
"transcript": "ENST00000636945.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs756127631",
"effect": "missense_variant",
"frequency_reference_population": 0.000033476124,
"gene_hgnc_id": 10596,
"gene_symbol": "SCN8A",
"gnomad_exomes_ac": 53,
"gnomad_exomes_af": 0.0000362795,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656996,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Developmental and epileptic encephalopathy, 13;Cognitive impairment with or without cerebellar ataxia;Seizures, benign familial infantile, 5|Developmental and epileptic encephalopathy|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.034,
"pos": 51769127,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.713,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014191.4"
}
]
}