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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: 19-19526257-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=19526257&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NDUFA13",
"hgnc_id": 17194,
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 15,
"score": 15,
"transcript": "NM_015965.7",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000258674",
"hgnc_id": null,
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"inheritance_mode": "",
"pathogenic_score": 15,
"score": 15,
"transcript": "ENST00000555938.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PP3,PP5_Very_Strong",
"acmg_score": 15,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": 0.2494,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.08,
"chr": "19",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": " nuclear type 28,Mitochondrial complex I deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8014538884162903,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 144,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 521,
"cdna_start": 184,
"cds_end": null,
"cds_length": 435,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_015965.7",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000507754.9",
"protein_coding": true,
"protein_id": "NP_057049.5",
"strand": true,
"transcript": "NM_015965.7",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 144,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 521,
"cdna_start": 184,
"cds_end": null,
"cds_length": 435,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000507754.9",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015965.7",
"protein_coding": true,
"protein_id": "ENSP00000423673.1",
"strand": true,
"transcript": "ENST00000507754.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 273,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1100,
"cdna_start": 182,
"cds_end": null,
"cds_length": 822,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000555938.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258674",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452549.1",
"strand": true,
"transcript": "ENST00000555938.1",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 169,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 598,
"cdna_start": 186,
"cds_end": null,
"cds_length": 510,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000911745.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581804.1",
"strand": true,
"transcript": "ENST00000911745.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 150,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 576,
"cdna_start": 179,
"cds_end": null,
"cds_length": 453,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000428459.6",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465129.1",
"strand": true,
"transcript": "ENST00000428459.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 143,
"aa_ref": "R",
"aa_start": 56,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 518,
"cdna_start": 181,
"cds_end": null,
"cds_length": 432,
"cds_start": 167,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000941958.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.167G>A",
"hgvs_p": "p.Arg56His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612017.1",
"strand": true,
"transcript": "ENST00000941958.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 141,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 508,
"cdna_start": 184,
"cds_end": null,
"cds_length": 426,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000941959.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612018.1",
"strand": true,
"transcript": "ENST00000941959.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 137,
"aa_ref": "R",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 500,
"cdna_start": 163,
"cds_end": null,
"cds_length": 414,
"cds_start": 149,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000911746.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581805.1",
"strand": true,
"transcript": "ENST00000911746.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 135,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 505,
"cdna_start": 198,
"cds_end": null,
"cds_length": 408,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000911743.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581802.1",
"strand": true,
"transcript": "ENST00000911743.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 120,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 825,
"cdna_start": 181,
"cds_end": null,
"cds_length": 363,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000503283.5",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468317.1",
"strand": true,
"transcript": "ENST00000503283.5",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 120,
"aa_ref": "R",
"aa_start": 57,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 443,
"cdna_start": 179,
"cds_end": null,
"cds_length": 363,
"cds_start": 170,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000880579.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.170G>A",
"hgvs_p": "p.Arg57His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550638.1",
"strand": true,
"transcript": "ENST00000880579.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 138,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 515,
"cdna_start": null,
"cds_end": null,
"cds_length": 417,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000911742.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.155+15G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581801.1",
"strand": true,
"transcript": "ENST00000911742.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 73,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 310,
"cdna_start": null,
"cds_end": null,
"cds_length": 222,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000911744.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "c.16-1079G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581803.1",
"strand": true,
"transcript": "ENST00000911744.1",
"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": 1166,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000502506.6",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "n.*3G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467274.2",
"strand": true,
"transcript": "ENST00000502506.6",
"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": 593,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000511180.4",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "n.168G>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": "ENST00000511180.4",
"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": 640,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000511584.2",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "n.179G>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": "ENST00000511584.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1071,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000586674.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258674",
"hgvs_c": "n.180G>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": "ENST00000586674.1",
"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": 502,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000606722.1",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "n.146G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476093.2",
"strand": true,
"transcript": "ENST00000606722.1",
"transcript_support_level": 3
},
{
"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": 1166,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000502506.6",
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"hgvs_c": "n.*3G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467274.2",
"strand": true,
"transcript": "ENST00000502506.6",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs752513525",
"effect": "missense_variant",
"frequency_reference_population": 0.000009294025,
"gene_hgnc_id": 17194,
"gene_symbol": "NDUFA13",
"gnomad_exomes_ac": 14,
"gnomad_exomes_af": 0.00000957786,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656875,
"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": "Likely pathogenic",
"phenotype_combined": "Mitochondrial complex I deficiency|Mitochondrial complex I deficiency, nuclear type 28|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.401,
"pos": 19526257,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.655,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_015965.7"
}
]
}