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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: 3-13319901-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=13319901&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 13319901,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024923.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"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.5245G>A",
"hgvs_p": "p.Val1749Ile",
"transcript": "NM_024923.4",
"protein_id": "NP_079199.2",
"transcript_support_level": null,
"aa_start": 1749,
"aa_end": null,
"aa_length": 1887,
"cds_start": 5245,
"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": "V",
"aa_alt": "I",
"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.5245G>A",
"hgvs_p": "p.Val1749Ile",
"transcript": "ENST00000254508.7",
"protein_id": "ENSP00000254508.5",
"transcript_support_level": 2,
"aa_start": 1749,
"aa_end": null,
"aa_length": 1887,
"cds_start": 5245,
"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": "V",
"aa_alt": "I",
"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.5272G>A",
"hgvs_p": "p.Val1758Ile",
"transcript": "ENST00000916956.1",
"protein_id": "ENSP00000587015.1",
"transcript_support_level": null,
"aa_start": 1758,
"aa_end": null,
"aa_length": 1896,
"cds_start": 5272,
"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": "V",
"aa_alt": "I",
"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.5233G>A",
"hgvs_p": "p.Val1745Ile",
"transcript": "ENST00000916951.1",
"protein_id": "ENSP00000587010.1",
"transcript_support_level": null,
"aa_start": 1745,
"aa_end": null,
"aa_length": 1883,
"cds_start": 5233,
"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": "V",
"aa_alt": "I",
"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.5182G>A",
"hgvs_p": "p.Val1728Ile",
"transcript": "ENST00000916953.1",
"protein_id": "ENSP00000587012.1",
"transcript_support_level": null,
"aa_start": 1728,
"aa_end": null,
"aa_length": 1866,
"cds_start": 5182,
"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": "V",
"aa_alt": "I",
"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.5155G>A",
"hgvs_p": "p.Val1719Ile",
"transcript": "ENST00000916952.1",
"protein_id": "ENSP00000587011.1",
"transcript_support_level": null,
"aa_start": 1719,
"aa_end": null,
"aa_length": 1857,
"cds_start": 5155,
"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": "V",
"aa_alt": "I",
"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.5089G>A",
"hgvs_p": "p.Val1697Ile",
"transcript": "ENST00000916954.1",
"protein_id": "ENSP00000587013.1",
"transcript_support_level": null,
"aa_start": 1697,
"aa_end": null,
"aa_length": 1835,
"cds_start": 5089,
"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": "V",
"aa_alt": "I",
"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.5086G>A",
"hgvs_p": "p.Val1696Ile",
"transcript": "ENST00000916955.1",
"protein_id": "ENSP00000587014.1",
"transcript_support_level": null,
"aa_start": 1696,
"aa_end": null,
"aa_length": 1834,
"cds_start": 5086,
"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": "V",
"aa_alt": "I",
"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.5077G>A",
"hgvs_p": "p.Val1693Ile",
"transcript": "ENST00000916950.1",
"protein_id": "ENSP00000587009.1",
"transcript_support_level": null,
"aa_start": 1693,
"aa_end": null,
"aa_length": 1831,
"cds_start": 5077,
"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": "V",
"aa_alt": "I",
"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.2629G>A",
"hgvs_p": "p.Val877Ile",
"transcript": "XM_047447795.1",
"protein_id": "XP_047303751.1",
"transcript_support_level": null,
"aa_start": 877,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2629,
"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": "V",
"aa_alt": "I",
"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.2596G>A",
"hgvs_p": "p.Val866Ile",
"transcript": "XM_047447797.1",
"protein_id": "XP_047303753.1",
"transcript_support_level": null,
"aa_start": 866,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2596,
"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": "V",
"aa_alt": "I",
"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.2560G>A",
"hgvs_p": "p.Val854Ile",
"transcript": "XM_047447796.1",
"protein_id": "XP_047303752.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 992,
"cds_start": 2560,
"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.973G>A",
"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.*673G>A",
"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.*673G>A",
"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": "rs752865042",
"frequency_reference_population": 0.000015049547,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000150495,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2454550564289093,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.188,
"revel_prediction": "Benign",
"alphamissense_score": 0.1038,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.289,
"phylop100way_prediction": "Uncertain_significance",
"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_024923.4",
"gene_symbol": "NUP210",
"hgnc_id": 30052,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.5245G>A",
"hgvs_p": "p.Val1749Ile"
}
],
"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
}