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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: 3-100348880-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=100348880&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 100348880,
"ref": "C",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_020202.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.583C>G",
"hgvs_p": "p.Arg195Gly",
"transcript": "NM_020202.5",
"protein_id": "NP_064587.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 276,
"cds_start": 583,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000394140.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020202.5"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.583C>G",
"hgvs_p": "p.Arg195Gly",
"transcript": "ENST00000394140.9",
"protein_id": "ENSP00000377696.3",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 276,
"cds_start": 583,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020202.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394140.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "n.1138C>G",
"hgvs_p": null,
"transcript": "ENST00000465368.5",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000465368.5"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.508C>G",
"hgvs_p": "p.Arg170Gly",
"transcript": "ENST00000867930.1",
"protein_id": "ENSP00000537989.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 251,
"cds_start": 508,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867930.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.400C>G",
"hgvs_p": "p.Arg134Gly",
"transcript": "ENST00000867932.1",
"protein_id": "ENSP00000537991.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 215,
"cds_start": 400,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867932.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.343C>G",
"hgvs_p": "p.Arg115Gly",
"transcript": "ENST00000867931.1",
"protein_id": "ENSP00000537990.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 196,
"cds_start": 343,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867931.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "c.85C>G",
"hgvs_p": "p.Arg29Gly",
"transcript": "ENST00000867929.1",
"protein_id": "ENSP00000537988.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 110,
"cds_start": 85,
"cds_end": null,
"cds_length": 333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867929.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "n.524C>G",
"hgvs_p": null,
"transcript": "ENST00000478856.5",
"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": "ENST00000478856.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "n.*323C>G",
"hgvs_p": null,
"transcript": "ENST00000480073.5",
"protein_id": "ENSP00000419157.1",
"transcript_support_level": 3,
"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": "ENST00000480073.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"hgvs_c": "n.*323C>G",
"hgvs_p": null,
"transcript": "ENST00000480073.5",
"protein_id": "ENSP00000419157.1",
"transcript_support_level": 3,
"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": "ENST00000480073.5"
}
],
"gene_symbol": "NIT2",
"gene_hgnc_id": 29878,
"dbsnp": "rs751318008",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.97063148021698,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09200000017881393,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.914,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9813,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.057,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000320201018754287,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_020202.5",
"gene_symbol": "NIT2",
"hgnc_id": 29878,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.583C>G",
"hgvs_p": "p.Arg195Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}