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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: 3-138064725-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=138064725&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DZIP1L",
"hgnc_id": 26551,
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_173543.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.4543,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.02,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.522930383682251,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3492,
"cdna_start": 2407,
"cds_end": null,
"cds_length": 2304,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_173543.3",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000327532.7",
"protein_coding": true,
"protein_id": "NP_775814.2",
"strand": false,
"transcript": "NM_173543.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3492,
"cdna_start": 2407,
"cds_end": null,
"cds_length": 2304,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000327532.7",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_173543.3",
"protein_coding": true,
"protein_id": "ENSP00000332148.2",
"strand": false,
"transcript": "ENST00000327532.7",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3294,
"cdna_start": 2206,
"cds_end": null,
"cds_length": 2304,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000851674.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521733.1",
"strand": false,
"transcript": "ENST00000851674.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3591,
"cdna_start": 2506,
"cds_end": null,
"cds_length": 2304,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000912002.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582061.1",
"strand": false,
"transcript": "ENST00000912002.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3261,
"cdna_start": 2195,
"cds_end": null,
"cds_length": 2304,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000912003.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582062.1",
"strand": false,
"transcript": "ENST00000912003.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 720,
"aa_ref": "L",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3070,
"cdna_start": 1985,
"cds_end": null,
"cds_length": 2163,
"cds_start": 1904,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000851675.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.1904T>C",
"hgvs_p": "p.Leu635Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521734.1",
"strand": false,
"transcript": "ENST00000851675.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 713,
"aa_ref": "L",
"aa_start": 628,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3389,
"cdna_start": 2304,
"cds_end": null,
"cds_length": 2142,
"cds_start": 1883,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000965047.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.1883T>C",
"hgvs_p": "p.Leu628Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635106.1",
"strand": false,
"transcript": "ENST00000965047.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 147,
"aa_ref": "L",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 475,
"cdna_start": 153,
"cds_end": null,
"cds_length": 444,
"cds_start": 152,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000486487.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.152T>C",
"hgvs_p": "p.Leu51Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417228.1",
"strand": false,
"transcript": "ENST00000486487.1",
"transcript_support_level": 3
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 806,
"aa_ref": "L",
"aa_start": 710,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2505,
"cdna_start": 2186,
"cds_end": null,
"cds_length": 2421,
"cds_start": 2129,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_011512518.3",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2129T>C",
"hgvs_p": "p.Leu710Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011510820.1",
"strand": false,
"transcript": "XM_011512518.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 795,
"aa_ref": "L",
"aa_start": 710,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3271,
"cdna_start": 2186,
"cds_end": null,
"cds_length": 2388,
"cds_start": 2129,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_005247198.4",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2129T>C",
"hgvs_p": "p.Leu710Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005247255.1",
"strand": false,
"transcript": "XM_005247198.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 778,
"aa_ref": "L",
"aa_start": 682,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2726,
"cdna_start": 2407,
"cds_end": null,
"cds_length": 2337,
"cds_start": 2045,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_006713527.4",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.2045T>C",
"hgvs_p": "p.Leu682Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713590.1",
"strand": false,
"transcript": "XM_006713527.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 759,
"aa_ref": "L",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2364,
"cdna_start": 2045,
"cds_end": null,
"cds_length": 2280,
"cds_start": 1988,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_011512524.3",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.1988T>C",
"hgvs_p": "p.Leu663Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011510826.1",
"strand": false,
"transcript": "XM_011512524.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 748,
"aa_ref": "L",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 2045,
"cds_end": null,
"cds_length": 2247,
"cds_start": 1988,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047447642.1",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.1988T>C",
"hgvs_p": "p.Leu663Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303598.1",
"strand": false,
"transcript": "XM_047447642.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 478,
"aa_ref": "L",
"aa_start": 382,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2762,
"cdna_start": 2443,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1145,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_005247200.4",
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"hgvs_c": "c.1145T>C",
"hgvs_p": "p.Leu382Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005247257.1",
"strand": false,
"transcript": "XM_005247200.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1472123809",
"effect": "missense_variant",
"frequency_reference_population": 0.000006569698,
"gene_hgnc_id": 26551,
"gene_symbol": "DZIP1L",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065697,
"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 provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.887,
"pos": 138064725,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.234,
"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_173543.3"
}
]
}