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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: 12-55987007-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=55987007&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 55987007,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002868.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "NM_002868.4",
"protein_id": "NP_002859.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 215,
"cds_start": 47,
"cds_end": null,
"cds_length": 648,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 5273,
"mane_select": "ENST00000360299.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000360299.10",
"protein_id": "ENSP00000353444.5",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 215,
"cds_start": 47,
"cds_end": null,
"cds_length": 648,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 5273,
"mane_select": "NM_002868.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000553116.5",
"protein_id": "ENSP00000450168.1",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 215,
"cds_start": 47,
"cds_end": null,
"cds_length": 648,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 3322,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "n.47G>A",
"hgvs_p": null,
"transcript": "ENST00000549505.5",
"protein_id": "ENSP00000450285.1",
"transcript_support_level": 1,
"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": 3148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.290G>A",
"hgvs_p": "p.Ser97Asn",
"transcript": "NM_001414458.1",
"protein_id": "NP_001401387.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 296,
"cds_start": 290,
"cds_end": null,
"cds_length": 891,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 5576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "NM_001252036.2",
"protein_id": "NP_001238965.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 215,
"cds_start": 47,
"cds_end": null,
"cds_length": 648,
"cdna_start": 191,
"cdna_end": null,
"cdna_length": 5263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "NM_001414457.1",
"protein_id": "NP_001401386.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 215,
"cds_start": 47,
"cds_end": null,
"cds_length": 648,
"cdna_start": 304,
"cdna_end": null,
"cdna_length": 5376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "NM_001252037.2",
"protein_id": "NP_001238966.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 174,
"cds_start": 47,
"cds_end": null,
"cds_length": 525,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 5150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000448789.2",
"protein_id": "ENSP00000391319.2",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 174,
"cds_start": 47,
"cds_end": null,
"cds_length": 525,
"cdna_start": 178,
"cdna_end": null,
"cdna_length": 1530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000548068.5",
"protein_id": "ENSP00000447895.1",
"transcript_support_level": 4,
"aa_start": 16,
"aa_end": null,
"aa_length": 114,
"cds_start": 47,
"cds_end": null,
"cds_length": 345,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000551459.5",
"protein_id": "ENSP00000449554.1",
"transcript_support_level": 4,
"aa_start": 16,
"aa_end": null,
"aa_length": 99,
"cds_start": 47,
"cds_end": null,
"cds_length": 301,
"cdna_start": 315,
"cdna_end": null,
"cdna_length": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.152G>A",
"hgvs_p": "p.Ser51Asn",
"transcript": "ENST00000549915.5",
"protein_id": "ENSP00000449762.1",
"transcript_support_level": 4,
"aa_start": 51,
"aa_end": null,
"aa_length": 78,
"cds_start": 152,
"cds_end": null,
"cds_length": 237,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn",
"transcript": "ENST00000628569.1",
"protein_id": "ENSP00000487368.1",
"transcript_support_level": 5,
"aa_start": 16,
"aa_end": null,
"aa_length": 73,
"cds_start": 47,
"cds_end": null,
"cds_length": 222,
"cdna_start": 47,
"cdna_end": null,
"cdna_length": 496,
"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": "RAB5B",
"gene_hgnc_id": 9784,
"hgvs_c": "n.201G>A",
"hgvs_p": null,
"transcript": "ENST00000546810.1",
"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": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAB5B",
"gene_hgnc_id": 9784,
"dbsnp": "rs781689220",
"frequency_reference_population": 0.00001910344,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000191034,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11621561646461487,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.137,
"revel_prediction": "Benign",
"alphamissense_score": 0.149,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.075,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002868.4",
"gene_symbol": "RAB5B",
"hgnc_id": 9784,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.47G>A",
"hgvs_p": "p.Ser16Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}