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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: 2-206788032-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=206788032&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "FASTKD2",
"hgnc_id": 29160,
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_014929.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000299634",
"hgnc_id": null,
"hgvs_c": "n.114-1170G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 14,
"score": 14,
"transcript": "ENST00000765262.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 4,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.27,
"chr": "2",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " nuclear type 1,Combined oxidative phosphorylation deficiency 44,Mitochondrial complex IV deficiency",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.27000001072883606,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6712,
"cdna_start": 1882,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001136193.2",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000402774.8",
"protein_coding": true,
"protein_id": "NP_001129665.1",
"strand": true,
"transcript": "NM_001136193.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6712,
"cdna_start": 1882,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000402774.8",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001136193.2",
"protein_coding": true,
"protein_id": "ENSP00000385990.3",
"strand": true,
"transcript": "ENST00000402774.8",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3188,
"cdna_start": 2038,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000236980.10",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000236980.6",
"strand": true,
"transcript": "ENST00000236980.10",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6727,
"cdna_start": 1897,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001136194.2",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001129666.1",
"strand": true,
"transcript": "NM_001136194.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6619,
"cdna_start": 1789,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_014929.4",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_055744.2",
"strand": true,
"transcript": "NM_014929.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2344,
"cdna_start": 1897,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000403094.3",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384929.3",
"strand": true,
"transcript": "ENST00000403094.3",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2276,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000870595.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540654.1",
"strand": true,
"transcript": "ENST00000870595.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2519,
"cdna_start": 2006,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000966850.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636909.1",
"strand": true,
"transcript": "ENST00000966850.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 710,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2392,
"cdna_start": 1931,
"cds_end": null,
"cds_length": 2133,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000966852.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636911.1",
"strand": true,
"transcript": "ENST00000966852.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 704,
"aa_ref": "Q",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2378,
"cdna_start": 1865,
"cds_end": null,
"cds_length": 2115,
"cds_start": 1672,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000966851.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Gln558*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636910.1",
"strand": true,
"transcript": "ENST00000966851.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 702,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2353,
"cdna_start": 1790,
"cds_end": null,
"cds_length": 2109,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000870594.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540653.1",
"strand": true,
"transcript": "ENST00000870594.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 693,
"aa_ref": "Q",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2373,
"cdna_start": 1904,
"cds_end": null,
"cds_length": 2082,
"cds_start": 1690,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000966849.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1690C>T",
"hgvs_p": "p.Gln564*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636908.1",
"strand": true,
"transcript": "ENST00000966849.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 691,
"aa_ref": "Q",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2895,
"cdna_start": 1745,
"cds_end": null,
"cds_length": 2076,
"cds_start": 1633,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000870593.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1633C>T",
"hgvs_p": "p.Gln545*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540652.1",
"strand": true,
"transcript": "ENST00000870593.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 691,
"aa_ref": "Q",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4081,
"cdna_start": 1828,
"cds_end": null,
"cds_length": 2076,
"cds_start": 1633,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000918135.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1633C>T",
"hgvs_p": "p.Gln545*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588194.1",
"strand": true,
"transcript": "ENST00000918135.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 686,
"aa_ref": "Q",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": 1813,
"cds_end": null,
"cds_length": 2061,
"cds_start": 1618,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000870596.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1618C>T",
"hgvs_p": "p.Gln540*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540655.1",
"strand": true,
"transcript": "ENST00000870596.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 686,
"aa_ref": "Q",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2234,
"cdna_start": 1719,
"cds_end": null,
"cds_length": 2061,
"cds_start": 1618,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000918136.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "c.1618C>T",
"hgvs_p": "p.Gln540*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588195.1",
"strand": true,
"transcript": "ENST00000918136.1",
"transcript_support_level": null
},
{
"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": 842,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000471788.1",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "n.382C>T",
"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": "ENST00000471788.1",
"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": 4999,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000487777.5",
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"hgvs_c": "n.1748C>T",
"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": "ENST00000487777.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 421,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000765262.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000299634",
"hgvs_c": "n.114-1170G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000765262.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 645,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000765263.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000299634",
"hgvs_c": "n.340-1170G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000765263.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs755068980",
"effect": "stop_gained",
"frequency_reference_population": 0.000002479012,
"gene_hgnc_id": 29160,
"gene_symbol": "FASTKD2",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205284,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065722,
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Mitochondrial complex IV deficiency, nuclear type 1|Combined oxidative phosphorylation deficiency 44",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.185,
"pos": 206788032,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014929.4"
}
]
}