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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: 20-36606026-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=36606026&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 36606026,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_199483.3",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "NM_018840.5",
"protein_id": "NP_061328.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 129,
"cds_start": 75,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000344795.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018840.5"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "ENST00000344795.8",
"protein_id": "ENSP00000340164.3",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 129,
"cds_start": 75,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018840.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000344795.8"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "ENST00000373852.9",
"protein_id": "ENSP00000362958.5",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 137,
"cds_start": 75,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373852.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TGIF2-RAB5IF",
"gene_hgnc_id": 44664,
"hgvs_c": "c.193-1689G>A",
"hgvs_p": null,
"transcript": "ENST00000558530.1",
"protein_id": "ENSP00000454021.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000558530.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.75G>A",
"hgvs_p": null,
"transcript": "ENST00000483815.5",
"protein_id": "ENSP00000432510.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000483815.5"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "NM_199483.3",
"protein_id": "NP_955777.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 143,
"cds_start": 75,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_199483.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "ENST00000342422.3",
"protein_id": "ENSP00000341213.3",
"transcript_support_level": 2,
"aa_start": 25,
"aa_end": null,
"aa_length": 143,
"cds_start": 75,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342422.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "NM_001199534.2",
"protein_id": "NP_001186463.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 137,
"cds_start": 75,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199534.2"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "ENST00000948725.1",
"protein_id": "ENSP00000618784.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 123,
"cds_start": 75,
"cds_end": null,
"cds_length": 372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948725.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*",
"transcript": "NM_001374178.1",
"protein_id": "NP_001361107.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 121,
"cds_start": 75,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374178.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TGIF2-RAB5IF",
"gene_hgnc_id": 44664,
"hgvs_c": "c.193-1689G>A",
"hgvs_p": null,
"transcript": "NM_001199535.2",
"protein_id": "NP_001186464.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199535.2"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.216G>A",
"hgvs_p": null,
"transcript": "ENST00000491113.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000491113.1"
},
{
"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": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.75G>A",
"hgvs_p": null,
"transcript": "ENST00000492721.5",
"protein_id": "ENSP00000435871.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000492721.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.248G>A",
"hgvs_p": null,
"transcript": "NR_026562.4",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_026562.4"
},
{
"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": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.248G>A",
"hgvs_p": null,
"transcript": "NR_164350.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_164350.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"hgvs_c": "n.248G>A",
"hgvs_p": null,
"transcript": "NR_164351.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_164351.1"
}
],
"gene_symbol": "RAB5IF",
"gene_hgnc_id": 15870,
"dbsnp": "rs1464308137",
"frequency_reference_population": 0.00000145337,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000145337,
"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": 0.7451563477516174,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.28999999165534973,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.1512,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.596,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.29,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_199483.3",
"gene_symbol": "RAB5IF",
"hgnc_id": 15870,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Trp25*"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001199535.2",
"gene_symbol": "TGIF2-RAB5IF",
"hgnc_id": 44664,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.193-1689G>A",
"hgvs_p": null
}
],
"clinvar_disease": " and impaired intellectual development 1, and impaired intellectual development syndrome 2, skeletal anomalies,10 conditions,Craniofacial dysmorphism",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2|10 conditions|Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}