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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: 3-13319781-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=13319781&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 13319781,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_024923.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5365C>T",
"hgvs_p": "p.Arg1789Cys",
"transcript": "NM_024923.4",
"protein_id": "NP_079199.2",
"transcript_support_level": null,
"aa_start": 1789,
"aa_end": null,
"aa_length": 1887,
"cds_start": 5365,
"cds_end": null,
"cds_length": 5664,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000254508.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024923.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5365C>T",
"hgvs_p": "p.Arg1789Cys",
"transcript": "ENST00000254508.7",
"protein_id": "ENSP00000254508.5",
"transcript_support_level": 2,
"aa_start": 1789,
"aa_end": null,
"aa_length": 1887,
"cds_start": 5365,
"cds_end": null,
"cds_length": 5664,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024923.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254508.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5392C>T",
"hgvs_p": "p.Arg1798Cys",
"transcript": "ENST00000916956.1",
"protein_id": "ENSP00000587015.1",
"transcript_support_level": null,
"aa_start": 1798,
"aa_end": null,
"aa_length": 1896,
"cds_start": 5392,
"cds_end": null,
"cds_length": 5691,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916956.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5353C>T",
"hgvs_p": "p.Arg1785Cys",
"transcript": "ENST00000916951.1",
"protein_id": "ENSP00000587010.1",
"transcript_support_level": null,
"aa_start": 1785,
"aa_end": null,
"aa_length": 1883,
"cds_start": 5353,
"cds_end": null,
"cds_length": 5652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916951.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5302C>T",
"hgvs_p": "p.Arg1768Cys",
"transcript": "ENST00000916953.1",
"protein_id": "ENSP00000587012.1",
"transcript_support_level": null,
"aa_start": 1768,
"aa_end": null,
"aa_length": 1866,
"cds_start": 5302,
"cds_end": null,
"cds_length": 5601,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916953.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5275C>T",
"hgvs_p": "p.Arg1759Cys",
"transcript": "ENST00000916952.1",
"protein_id": "ENSP00000587011.1",
"transcript_support_level": null,
"aa_start": 1759,
"aa_end": null,
"aa_length": 1857,
"cds_start": 5275,
"cds_end": null,
"cds_length": 5574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916952.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5209C>T",
"hgvs_p": "p.Arg1737Cys",
"transcript": "ENST00000916954.1",
"protein_id": "ENSP00000587013.1",
"transcript_support_level": null,
"aa_start": 1737,
"aa_end": null,
"aa_length": 1835,
"cds_start": 5209,
"cds_end": null,
"cds_length": 5508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916954.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5206C>T",
"hgvs_p": "p.Arg1736Cys",
"transcript": "ENST00000916955.1",
"protein_id": "ENSP00000587014.1",
"transcript_support_level": null,
"aa_start": 1736,
"aa_end": null,
"aa_length": 1834,
"cds_start": 5206,
"cds_end": null,
"cds_length": 5505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916955.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.5197C>T",
"hgvs_p": "p.Arg1733Cys",
"transcript": "ENST00000916950.1",
"protein_id": "ENSP00000587009.1",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 1831,
"cds_start": 5197,
"cds_end": null,
"cds_length": 5496,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916950.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.2749C>T",
"hgvs_p": "p.Arg917Cys",
"transcript": "XM_047447795.1",
"protein_id": "XP_047303751.1",
"transcript_support_level": null,
"aa_start": 917,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2749,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447795.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.2716C>T",
"hgvs_p": "p.Arg906Cys",
"transcript": "XM_047447797.1",
"protein_id": "XP_047303753.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2716,
"cds_end": null,
"cds_length": 3015,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447797.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "c.2680C>T",
"hgvs_p": "p.Arg894Cys",
"transcript": "XM_047447796.1",
"protein_id": "XP_047303752.1",
"transcript_support_level": null,
"aa_start": 894,
"aa_end": null,
"aa_length": 992,
"cds_start": 2680,
"cds_end": null,
"cds_length": 2979,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447796.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "n.1093C>T",
"hgvs_p": null,
"transcript": "ENST00000695489.1",
"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": "retained_intron",
"feature": "ENST00000695489.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "n.*793C>T",
"hgvs_p": null,
"transcript": "ENST00000695490.1",
"protein_id": "ENSP00000511960.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000695490.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"hgvs_c": "n.*793C>T",
"hgvs_p": null,
"transcript": "ENST00000695490.1",
"protein_id": "ENSP00000511960.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000695490.1"
}
],
"gene_symbol": "NUP210",
"gene_hgnc_id": 30052,
"dbsnp": "rs148214795",
"frequency_reference_population": 0.00003283763,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000348874,
"gnomad_genomes_af": 0.0000131442,
"gnomad_exomes_ac": 51,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5977479219436646,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.084,
"revel_prediction": "Benign",
"alphamissense_score": 0.1407,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.112,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024923.4",
"gene_symbol": "NUP210",
"hgnc_id": 30052,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.5365C>T",
"hgvs_p": "p.Arg1789Cys"
}
],
"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
}