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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: 19-5696298-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=5696298&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 5696298,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004793.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1847A>G",
"hgvs_p": "p.Asn616Ser",
"transcript": "NM_004793.4",
"protein_id": "NP_004784.2",
"transcript_support_level": null,
"aa_start": 616,
"aa_end": null,
"aa_length": 959,
"cds_start": 1847,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": "ENST00000360614.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004793.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1847A>G",
"hgvs_p": "p.Asn616Ser",
"transcript": "ENST00000360614.8",
"protein_id": "ENSP00000353826.2",
"transcript_support_level": 1,
"aa_start": 616,
"aa_end": null,
"aa_length": 959,
"cds_start": 1847,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": "NM_004793.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360614.8"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1457A>G",
"hgvs_p": "p.Asn486Ser",
"transcript": "ENST00000590729.5",
"protein_id": "ENSP00000465139.1",
"transcript_support_level": 1,
"aa_start": 486,
"aa_end": null,
"aa_length": 829,
"cds_start": 1457,
"cds_end": null,
"cds_length": 2490,
"cdna_start": 1516,
"cdna_end": null,
"cdna_length": 2626,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590729.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1847A>G",
"hgvs_p": "p.Asn616Ser",
"transcript": "ENST00000958482.1",
"protein_id": "ENSP00000628541.1",
"transcript_support_level": null,
"aa_start": 616,
"aa_end": null,
"aa_length": 1021,
"cds_start": 1847,
"cds_end": null,
"cds_length": 3066,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 3276,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958482.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1994A>G",
"hgvs_p": "p.Asn665Ser",
"transcript": "ENST00000877980.1",
"protein_id": "ENSP00000548039.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 1008,
"cds_start": 1994,
"cds_end": null,
"cds_length": 3027,
"cdna_start": 2008,
"cdna_end": null,
"cdna_length": 3236,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877980.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1847A>G",
"hgvs_p": "p.Asn616Ser",
"transcript": "ENST00000913306.1",
"protein_id": "ENSP00000583365.1",
"transcript_support_level": null,
"aa_start": 616,
"aa_end": null,
"aa_length": 958,
"cds_start": 1847,
"cds_end": null,
"cds_length": 2877,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 3089,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913306.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1655A>G",
"hgvs_p": "p.Asn552Ser",
"transcript": "NM_001276479.2",
"protein_id": "NP_001263408.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 895,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001276479.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1655A>G",
"hgvs_p": "p.Asn552Ser",
"transcript": "ENST00000593119.5",
"protein_id": "ENSP00000468541.1",
"transcript_support_level": 2,
"aa_start": 552,
"aa_end": null,
"aa_length": 895,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 1688,
"cdna_end": null,
"cdna_length": 2918,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593119.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1607A>G",
"hgvs_p": "p.Asn536Ser",
"transcript": "ENST00000877979.1",
"protein_id": "ENSP00000548038.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 879,
"cds_start": 1607,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 1621,
"cdna_end": null,
"cdna_length": 2850,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877979.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1505A>G",
"hgvs_p": "p.Asn502Ser",
"transcript": "ENST00000585374.5",
"protein_id": "ENSP00000465585.1",
"transcript_support_level": 5,
"aa_start": 502,
"aa_end": null,
"aa_length": 845,
"cds_start": 1505,
"cds_end": null,
"cds_length": 2538,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 2882,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000585374.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1259A>G",
"hgvs_p": "p.Asn420Ser",
"transcript": "NM_001276480.1",
"protein_id": "NP_001263409.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 763,
"cds_start": 1259,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001276480.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1259A>G",
"hgvs_p": "p.Asn420Ser",
"transcript": "ENST00000540670.6",
"protein_id": "ENSP00000441523.1",
"transcript_support_level": 2,
"aa_start": 420,
"aa_end": null,
"aa_length": 763,
"cds_start": 1259,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1772,
"cdna_end": null,
"cdna_length": 3002,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540670.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.1585A>G",
"hgvs_p": null,
"transcript": "ENST00000587552.5",
"protein_id": null,
"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": 2816,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000587552.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.*1096A>G",
"hgvs_p": null,
"transcript": "ENST00000590558.5",
"protein_id": "ENSP00000467808.1",
"transcript_support_level": 5,
"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": 2884,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000590558.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.1652A>G",
"hgvs_p": null,
"transcript": "NR_076392.2",
"protein_id": null,
"transcript_support_level": null,
"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": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_076392.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.*1096A>G",
"hgvs_p": null,
"transcript": "ENST00000590558.5",
"protein_id": "ENSP00000467808.1",
"transcript_support_level": 5,
"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": 2884,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000590558.5"
}
],
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"dbsnp": "rs200839886",
"frequency_reference_population": 0.000001368813,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136881,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.968420147895813,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.851,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.875,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.44,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_004793.4",
"gene_symbol": "LONP1",
"hgnc_id": 9479,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,XL",
"hgvs_c": "c.1847A>G",
"hgvs_p": "p.Asn616Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}