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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: 3-49022448-C-CT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49022448&ref=C&alt=CT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49022448,
"ref": "C",
"alt": "CT",
"effect": "frameshift_variant,stop_gained",
"transcript": "ENST00000326925.11",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.180_181insT",
"hgvs_p": "p.Asp61fs",
"transcript": "NM_199069.2",
"protein_id": "NP_951032.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 184,
"cds_start": 181,
"cds_end": null,
"cds_length": 555,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 902,
"mane_select": "ENST00000326925.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.180_181insT",
"hgvs_p": "p.Asp61fs",
"transcript": "ENST00000326925.11",
"protein_id": "ENSP00000323076.5",
"transcript_support_level": 1,
"aa_start": 61,
"aa_end": null,
"aa_length": 184,
"cds_start": 181,
"cds_end": null,
"cds_length": 555,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 902,
"mane_select": "NM_199069.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "ENST00000451378.2",
"protein_id": "ENSP00000402465.2",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "NM_199070.2",
"protein_id": "NP_951033.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "NM_199073.2",
"protein_id": "NP_951047.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 1117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "NM_199074.2",
"protein_id": "NP_951056.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "ENST00000326912.8",
"protein_id": "ENSP00000323003.4",
"transcript_support_level": 2,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 216,
"cdna_end": null,
"cdna_length": 705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "c.9_10insT",
"hgvs_p": "p.Asp4fs",
"transcript": "ENST00000395458.6",
"protein_id": "ENSP00000378843.2",
"transcript_support_level": 2,
"aa_start": 4,
"aa_end": null,
"aa_length": 127,
"cds_start": 10,
"cds_end": null,
"cds_length": 384,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 808,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "n.204_205insT",
"hgvs_p": null,
"transcript": "ENST00000480392.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 769,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"hgvs_c": "n.336_337insT",
"hgvs_p": null,
"transcript": "ENST00000496152.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DALRD3",
"gene_hgnc_id": 25536,
"hgvs_c": "c.-778_-777insA",
"hgvs_p": null,
"transcript": "ENST00000496568.1",
"protein_id": "ENSP00000485305.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 71,
"cds_start": -4,
"cds_end": null,
"cds_length": 217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DALRD3",
"gene_hgnc_id": 25536,
"hgvs_c": "n.-158_-157insA",
"hgvs_p": null,
"transcript": "ENST00000492585.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NDUFAF3",
"gene_hgnc_id": 29918,
"dbsnp": "rs752864722",
"frequency_reference_population": 0.000044019107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 71,
"gnomad_exomes_af": 0.0000444983,
"gnomad_genomes_af": 0.0000394203,
"gnomad_exomes_ac": 65,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.043,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000326925.11",
"gene_symbol": "NDUFAF3",
"hgnc_id": 29918,
"effects": [
"frameshift_variant",
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.180_181insT",
"hgvs_p": "p.Asp61fs"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000496568.1",
"gene_symbol": "DALRD3",
"hgnc_id": 25536,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,Unknown,AD",
"hgvs_c": "c.-778_-777insA",
"hgvs_p": null
}
],
"clinvar_disease": "Mitochondrial complex I deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Mitochondrial complex I deficiency|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}