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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: 9-136722267-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136722267&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DIPK1B",
"hgnc_id": 28290,
"hgvs_c": "c.449A>C",
"hgvs_p": "p.Lys150Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_152421.4",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SNHG7",
"hgnc_id": 28254,
"hgvs_c": "n.1456T>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000414282.5",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "LOC124900276",
"hgnc_id": null,
"hgvs_c": "c.-1992T>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "XM_047424334.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 153,
"alphamissense_prediction": null,
"alphamissense_score": 0.1468,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.46,
"chr": "9",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08409133553504944,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 431,
"aa_ref": "K",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2358,
"cdna_start": 543,
"cds_end": null,
"cds_length": 1296,
"cds_start": 449,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_152421.4",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.449A>C",
"hgvs_p": "p.Lys150Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371692.9",
"protein_coding": true,
"protein_id": "NP_689634.2",
"strand": true,
"transcript": "NM_152421.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 431,
"aa_ref": "K",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2358,
"cdna_start": 543,
"cds_end": null,
"cds_length": 1296,
"cds_start": 449,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000371692.9",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.449A>C",
"hgvs_p": "p.Lys150Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152421.4",
"protein_coding": true,
"protein_id": "ENSP00000360757.4",
"strand": true,
"transcript": "ENST00000371692.9",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 344,
"aa_ref": "K",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2410,
"cdna_start": 1287,
"cds_end": null,
"cds_length": 1035,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000371691.5",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.188A>C",
"hgvs_p": "p.Lys63Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000360756.1",
"strand": true,
"transcript": "ENST00000371691.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 407,
"aa_ref": "K",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2314,
"cdna_start": 525,
"cds_end": null,
"cds_length": 1224,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000931511.1",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.377A>C",
"hgvs_p": "p.Lys126Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601570.1",
"strand": true,
"transcript": "ENST00000931511.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 379,
"aa_ref": "K",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1565,
"cdna_start": 584,
"cds_end": null,
"cds_length": 1140,
"cds_start": 449,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000942171.1",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.449A>C",
"hgvs_p": "p.Lys150Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612230.1",
"strand": true,
"transcript": "ENST00000942171.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 311,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7226,
"cdna_start": null,
"cds_end": null,
"cds_length": 936,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047424334.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124900276",
"hgvs_c": "c.-1992T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047280290.1",
"strand": false,
"transcript": "XM_047424334.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 407,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2260,
"cdna_start": null,
"cds_end": null,
"cds_length": 1224,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931512.1",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.411+38A>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601571.1",
"strand": true,
"transcript": "ENST00000931512.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 372,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1489,
"cdna_start": null,
"cds_end": null,
"cds_length": 1119,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931513.1",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.306+239A>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601572.1",
"strand": true,
"transcript": "ENST00000931513.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 291,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2016,
"cdna_start": null,
"cds_end": null,
"cds_length": 876,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931510.1",
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"hgvs_c": "c.64-695A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601569.1",
"strand": true,
"transcript": "ENST00000931510.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2357,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000414282.5",
"gene_hgnc_id": 28254,
"gene_symbol": "SNHG7",
"hgvs_c": "n.1456T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000414282.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs202223684",
"effect": "missense_variant",
"frequency_reference_population": 0.00009480881,
"gene_hgnc_id": 28290,
"gene_symbol": "DIPK1B",
"gnomad_exomes_ac": 135,
"gnomad_exomes_af": 0.0000923734,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 18,
"gnomad_genomes_af": 0.000118177,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.448,
"pos": 136722267,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.054,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_152421.4"
}
]
}