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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: 12-123253883-CA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123253883&ref=CA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123253883,
"ref": "CA",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000253233.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "NM_152269.5",
"protein_id": "NP_689482.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 1554,
"mane_select": "ENST00000253233.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000253233.6",
"protein_id": "ENSP00000253233.1",
"transcript_support_level": 1,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 1554,
"mane_select": "NM_152269.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "NM_001143905.2",
"protein_id": "NP_001137377.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "NM_001194995.1",
"protein_id": "NP_001181924.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 682,
"cdna_end": null,
"cdna_length": 1901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000366329.7",
"protein_id": "ENSP00000390647.1",
"transcript_support_level": 2,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 717,
"cdna_end": null,
"cdna_length": 2056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000429587.2",
"protein_id": "ENSP00000391513.2",
"transcript_support_level": 2,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 495,
"cdna_end": null,
"cdna_length": 1326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000536130.2",
"protein_id": "ENSP00000443072.2",
"transcript_support_level": 3,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 493,
"cdna_end": null,
"cdna_length": 1682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000543139.2",
"protein_id": "ENSP00000444843.2",
"transcript_support_level": 2,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 3528,
"cdna_end": null,
"cdna_length": 3819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000679849.1",
"protein_id": "ENSP00000505808.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "ENST00000546132.2",
"protein_id": "ENSP00000441796.2",
"transcript_support_level": 4,
"aa_start": 70,
"aa_end": null,
"aa_length": 119,
"cds_start": 210,
"cds_end": null,
"cds_length": 360,
"cdna_start": 321,
"cdna_end": null,
"cdna_length": 3022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "XM_011538980.4",
"protein_id": "XP_011537282.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 322,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "XM_024449273.2",
"protein_id": "XP_024305041.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 645,
"cdna_end": null,
"cdna_length": 1865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs",
"transcript": "XM_047429877.1",
"protein_id": "XP_047285833.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 210,
"cds_end": null,
"cds_length": 501,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 1927,
"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": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.210delA",
"hgvs_p": null,
"transcript": "ENST00000425637.3",
"protein_id": "ENSP00000506680.1",
"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": 2648,
"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": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.210delA",
"hgvs_p": null,
"transcript": "ENST00000538888.6",
"protein_id": "ENSP00000505059.1",
"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": 1634,
"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": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.210delA",
"hgvs_p": null,
"transcript": "ENST00000680325.1",
"protein_id": "ENSP00000505277.1",
"transcript_support_level": null,
"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": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.810-1342delT",
"hgvs_p": null,
"transcript": "ENST00000541002.7",
"protein_id": null,
"transcript_support_level": 5,
"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": 1110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.281-1342delT",
"hgvs_p": null,
"transcript": "ENST00000543217.6",
"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": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.*956-1342delT",
"hgvs_p": null,
"transcript": "ENST00000652466.1",
"protein_id": "ENSP00000498286.1",
"transcript_support_level": null,
"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": 3828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"dbsnp": "rs576462794",
"frequency_reference_population": 0.00021744652,
"hom_count_reference_population": 0,
"allele_count_reference_population": 351,
"gnomad_exomes_af": 0.000223684,
"gnomad_genomes_af": 0.000157575,
"gnomad_exomes_ac": 327,
"gnomad_genomes_ac": 24,
"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,
"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": -3.367,
"phylop100way_prediction": "Benign",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000253233.6",
"gene_symbol": "MTRFR",
"hgnc_id": 26784,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.210delA",
"hgvs_p": "p.Gly72fs"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000543217.6",
"gene_symbol": "CDK2AP1",
"hgnc_id": 14002,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.281-1342delT",
"hgvs_p": null
}
],
"clinvar_disease": "Combined oxidative phosphorylation defect type 7,Spastic paraplegia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1 O:1",
"phenotype_combined": "Combined oxidative phosphorylation defect type 7|not provided|Spastic paraplegia;Combined oxidative phosphorylation defect type 7",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}