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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: 16-2039932-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2039932&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2039932,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002528.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Gly303Ser",
"transcript": "NM_002528.7",
"protein_id": "NP_002519.2",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 304,
"cds_start": 907,
"cds_end": null,
"cds_length": 915,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "ENST00000651570.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Gly303Ser",
"transcript": "ENST00000651570.2",
"protein_id": "ENSP00000498421.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 304,
"cds_start": 907,
"cds_end": null,
"cds_length": 915,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "NM_002528.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.931G>A",
"hgvs_p": "p.Gly311Ser",
"transcript": "ENST00000219066.5",
"protein_id": "ENSP00000219066.1",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 312,
"cds_start": 931,
"cds_end": null,
"cds_length": 939,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 1067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.736G>A",
"hgvs_p": "p.Gly246Ser",
"transcript": "NM_001318193.2",
"protein_id": "NP_001305122.2",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 247,
"cds_start": 736,
"cds_end": null,
"cds_length": 744,
"cdna_start": 747,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.700G>A",
"hgvs_p": "p.Gly234Ser",
"transcript": "ENST00000566380.5",
"protein_id": "ENSP00000455267.1",
"transcript_support_level": 3,
"aa_start": 234,
"aa_end": null,
"aa_length": 235,
"cds_start": 700,
"cds_end": null,
"cds_length": 708,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Gly231Ser",
"transcript": "ENST00000651583.1",
"protein_id": "ENSP00000498821.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 232,
"cds_start": 691,
"cds_end": null,
"cds_length": 699,
"cdna_start": 691,
"cdna_end": null,
"cdna_length": 802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Gly207Ser",
"transcript": "ENST00000651522.1",
"protein_id": "ENSP00000498290.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 208,
"cds_start": 619,
"cds_end": null,
"cds_length": 627,
"cdna_start": 619,
"cdna_end": null,
"cdna_length": 733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Gly193Ser",
"transcript": "NM_001318194.2",
"protein_id": "NP_001305123.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 194,
"cds_start": 577,
"cds_end": null,
"cds_length": 585,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.628G>A",
"hgvs_p": "p.Gly210Ser",
"transcript": "XM_047434171.1",
"protein_id": "XP_047290127.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 211,
"cds_start": 628,
"cds_end": null,
"cds_length": 636,
"cdna_start": 943,
"cdna_end": null,
"cdna_length": 1055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.*317G>A",
"hgvs_p": null,
"transcript": "ENST00000561841.1",
"protein_id": "ENSP00000456301.1",
"transcript_support_level": 5,
"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": 1052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.452G>A",
"hgvs_p": null,
"transcript": "ENST00000561862.5",
"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": 564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.412G>A",
"hgvs_p": null,
"transcript": "ENST00000562951.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.579G>A",
"hgvs_p": null,
"transcript": "ENST00000565406.5",
"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": 691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.459G>A",
"hgvs_p": null,
"transcript": "ENST00000567727.5",
"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": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.*425G>A",
"hgvs_p": null,
"transcript": "ENST00000568513.5",
"protein_id": "ENSP00000457818.1",
"transcript_support_level": 3,
"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": 837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.*317G>A",
"hgvs_p": null,
"transcript": "ENST00000561841.1",
"protein_id": "ENSP00000456301.1",
"transcript_support_level": 5,
"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": 1052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.*425G>A",
"hgvs_p": null,
"transcript": "ENST00000568513.5",
"protein_id": "ENSP00000457818.1",
"transcript_support_level": 3,
"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": 837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"dbsnp": "rs375024045",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03687664866447449,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.026,
"revel_prediction": "Benign",
"alphamissense_score": 0.0706,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.146,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_002528.7",
"gene_symbol": "NTHL1",
"hgnc_id": 8028,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Gly303Ser"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}