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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: 5-38481601-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=38481601&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 38481601,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002310.6",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "NM_001127671.2",
"protein_id": "NP_001121143.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3620,
"cdna_end": null,
"cdna_length": 10553,
"mane_select": "ENST00000453190.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127671.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "ENST00000453190.7",
"protein_id": "ENSP00000398368.2",
"transcript_support_level": 2,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3620,
"cdna_end": null,
"cdna_length": 10553,
"mane_select": "NM_001127671.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000453190.7"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "ENST00000263409.8",
"protein_id": "ENSP00000263409.4",
"transcript_support_level": 1,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3451,
"cdna_end": null,
"cdna_length": 10089,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263409.8"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "NM_001364297.2",
"protein_id": "NP_001351226.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3640,
"cdna_end": null,
"cdna_length": 10573,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001364297.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "NM_002310.6",
"protein_id": "NP_002301.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 10385,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002310.6"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "ENST00000872131.1",
"protein_id": "ENSP00000542190.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3729,
"cdna_end": null,
"cdna_length": 5095,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872131.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "ENST00000952493.1",
"protein_id": "ENSP00000622552.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3743,
"cdna_end": null,
"cdna_length": 5541,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952493.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3255C>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "NM_001364298.2",
"protein_id": "NP_001351227.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1086,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 3607,
"cdna_end": null,
"cdna_length": 10540,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001364298.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3255C>A",
"hgvs_p": "p.Asn1085Lys",
"transcript": "ENST00000872130.1",
"protein_id": "ENSP00000542189.1",
"transcript_support_level": null,
"aa_start": 1085,
"aa_end": null,
"aa_length": 1086,
"cds_start": 3255,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 3602,
"cdna_end": null,
"cdna_length": 5404,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872130.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3210C>A",
"hgvs_p": "p.Asn1070Lys",
"transcript": "ENST00000952492.1",
"protein_id": "ENSP00000622551.1",
"transcript_support_level": null,
"aa_start": 1070,
"aa_end": null,
"aa_length": 1071,
"cds_start": 3210,
"cds_end": null,
"cds_length": 3216,
"cdna_start": 3538,
"cdna_end": null,
"cdna_length": 5340,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952492.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3198C>A",
"hgvs_p": "p.Asn1066Lys",
"transcript": "ENST00000929709.1",
"protein_id": "ENSP00000599768.1",
"transcript_support_level": null,
"aa_start": 1066,
"aa_end": null,
"aa_length": 1067,
"cds_start": 3198,
"cds_end": null,
"cds_length": 3204,
"cdna_start": 3544,
"cdna_end": null,
"cdna_length": 10182,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929709.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3195C>A",
"hgvs_p": "p.Asn1065Lys",
"transcript": "ENST00000952491.1",
"protein_id": "ENSP00000622550.1",
"transcript_support_level": null,
"aa_start": 1065,
"aa_end": null,
"aa_length": 1066,
"cds_start": 3195,
"cds_end": null,
"cds_length": 3201,
"cdna_start": 3603,
"cdna_end": null,
"cdna_length": 5401,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952491.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3342C>A",
"hgvs_p": "p.Asn1114Lys",
"transcript": "XM_047417172.1",
"protein_id": "XP_047273128.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1115,
"cds_start": 3342,
"cds_end": null,
"cds_length": 3348,
"cdna_start": 3689,
"cdna_end": null,
"cdna_length": 10622,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417172.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "XM_011514042.4",
"protein_id": "XP_011512344.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3681,
"cdna_end": null,
"cdna_length": 10614,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514042.4"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys",
"transcript": "XM_017009463.2",
"protein_id": "XP_016864952.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3288,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3784,
"cdna_end": null,
"cdna_length": 10717,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009463.2"
}
],
"gene_symbol": "LIFR",
"gene_hgnc_id": 6597,
"dbsnp": "rs3729751",
"frequency_reference_population": 0.0018828273,
"hom_count_reference_population": 4,
"allele_count_reference_population": 3039,
"gnomad_exomes_af": 0.0018956,
"gnomad_genomes_af": 0.00176019,
"gnomad_exomes_ac": 2771,
"gnomad_genomes_ac": 268,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011234253644943237,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.251,
"revel_prediction": "Benign",
"alphamissense_score": 0.3246,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.331,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002310.6",
"gene_symbol": "LIFR",
"hgnc_id": 6597,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3288C>A",
"hgvs_p": "p.Asn1096Lys"
}
],
"clinvar_disease": "Congenital anomaly of kidney and urinary tract,LIFR-related disorder,Stuve-Wiedemann syndrome,Stüve-Wiedemann syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:3",
"phenotype_combined": "Stuve-Wiedemann syndrome|Congenital anomaly of kidney and urinary tract|not provided|Stüve-Wiedemann syndrome 1|not specified|LIFR-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}