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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: X-70454299-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=70454299&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DLG3",
"hgnc_id": 2902,
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"inheritance_mode": "XL",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_021120.4",
"verdict": "Benign"
},
{
"benign_score": 13,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DLG3-AS1",
"hgnc_id": 40182,
"hgvs_c": "n.84-993G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -13,
"transcript": "ENST00000424211.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Very_Strong,BS2",
"acmg_score": -13,
"allele_count_reference_population": 28,
"alphamissense_prediction": null,
"alphamissense_score": 0.8431,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "X",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.38341811299324036,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 817,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6042,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 2454,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_021120.4",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374360.8",
"protein_coding": true,
"protein_id": "NP_066943.2",
"strand": true,
"transcript": "NM_021120.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 817,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6042,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 2454,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000374360.8",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021120.4",
"protein_coding": true,
"protein_id": "ENSP00000363480.3",
"strand": true,
"transcript": "ENST00000374360.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 512,
"aa_ref": "A",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5090,
"cdna_start": 707,
"cds_end": null,
"cds_length": 1539,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000374355.8",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363475.3",
"strand": true,
"transcript": "ENST00000374355.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 849,
"aa_ref": "A",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6112,
"cdna_start": 1783,
"cds_end": null,
"cds_length": 2550,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000194900.8",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000194900.4",
"strand": true,
"transcript": "ENST00000194900.8",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 831,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6080,
"cdna_start": 1754,
"cds_end": null,
"cds_length": 2496,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000949779.1",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619838.1",
"strand": true,
"transcript": "ENST00000949779.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 512,
"aa_ref": "A",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5090,
"cdna_start": 707,
"cds_end": null,
"cds_length": 1539,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_020730.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_065781.1",
"strand": true,
"transcript": "NM_020730.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 849,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6138,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 2550,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_006724625.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724688.1",
"strand": true,
"transcript": "XM_006724625.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 835,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6096,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 2508,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011530883.2",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011529185.1",
"strand": true,
"transcript": "XM_011530883.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 831,
"aa_ref": "A",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6084,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 2496,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_006724626.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Ala463Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724689.1",
"strand": true,
"transcript": "XM_006724626.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 498,
"aa_ref": "A",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5048,
"cdna_start": 707,
"cds_end": null,
"cds_length": 1497,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017029322.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884811.1",
"strand": true,
"transcript": "XM_017029322.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 494,
"aa_ref": "A",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5036,
"cdna_start": 707,
"cds_end": null,
"cds_length": 1485,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017029323.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884812.1",
"strand": true,
"transcript": "XM_017029323.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 480,
"aa_ref": "A",
"aa_start": 126,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4994,
"cdna_start": 707,
"cds_end": null,
"cds_length": 1443,
"cds_start": 377,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017029324.3",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884813.1",
"strand": true,
"transcript": "XM_017029324.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 366,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4871,
"cdna_start": null,
"cds_end": null,
"cds_length": 1101,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_005262248.5",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "c.-62C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262305.1",
"strand": true,
"transcript": "XM_005262248.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4626,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000463252.5",
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"hgvs_c": "n.1787C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000463252.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 432,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000424211.1",
"gene_hgnc_id": 40182,
"gene_symbol": "DLG3-AS1",
"hgvs_c": "n.84-993G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000424211.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 484,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000431103.2",
"gene_hgnc_id": 40182,
"gene_symbol": "DLG3-AS1",
"hgvs_c": "n.134-993G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000431103.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 434,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_046586.1",
"gene_hgnc_id": 40182,
"gene_symbol": "DLG3-AS1",
"hgvs_c": "n.84-993G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_046586.1",
"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": 401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_109801.1",
"gene_hgnc_id": 40182,
"gene_symbol": "DLG3-AS1",
"hgvs_c": "n.51-993G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_109801.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs371545673",
"effect": "missense_variant",
"frequency_reference_population": 0.000023183855,
"gene_hgnc_id": 2902,
"gene_symbol": "DLG3",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00000821207,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 19,
"gnomad_genomes_af": 0.000169963,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 6,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.537,
"pos": 70454299,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.243,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_021120.4"
}
]
}