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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: 3-42735744-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=42735744&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CCDC13",
"hgnc_id": 26358,
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_144719.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000280571",
"hgnc_id": null,
"hgvs_c": "c.1403G>A",
"hgvs_p": "p.Arg468Gln",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000648550.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CCDC13-AS1",
"hgnc_id": 41142,
"hgvs_c": "n.84+3086C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000418161.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 8,
"alphamissense_prediction": null,
"alphamissense_score": 0.058,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.71,
"chr": "3",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09828969836235046,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5456,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_144719.4",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000310232.11",
"protein_coding": true,
"protein_id": "NP_653320.3",
"strand": false,
"transcript": "NM_144719.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5456,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000310232.11",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_144719.4",
"protein_coding": true,
"protein_id": "ENSP00000309836.6",
"strand": false,
"transcript": "ENST00000310232.11",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 738,
"aa_ref": "R",
"aa_start": 468,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5555,
"cdna_start": 1517,
"cds_end": null,
"cds_length": 2217,
"cds_start": 1403,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000648550.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000280571",
"hgvs_c": "c.1403G>A",
"hgvs_p": "p.Arg468Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496982.1",
"strand": false,
"transcript": "ENST00000648550.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 680,
"aa_ref": "R",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2709,
"cdna_start": 1298,
"cds_end": null,
"cds_length": 2043,
"cds_start": 1229,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000954780.1",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1229G>A",
"hgvs_p": "p.Arg410Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624839.1",
"strand": false,
"transcript": "ENST00000954780.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 674,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5333,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 2025,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005264898.4",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005264955.1",
"strand": false,
"transcript": "XM_005264898.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 646,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5249,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011533418.3",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531720.1",
"strand": false,
"transcript": "XM_011533418.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 495,
"aa_ref": "R",
"aa_start": 225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5467,
"cdna_start": 1429,
"cds_end": null,
"cds_length": 1488,
"cds_start": 674,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011533419.3",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.674G>A",
"hgvs_p": "p.Arg225Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531721.1",
"strand": false,
"transcript": "XM_011533419.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 495,
"aa_ref": "R",
"aa_start": 225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4847,
"cdna_start": 809,
"cds_end": null,
"cds_length": 1488,
"cds_start": 674,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017005781.2",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.674G>A",
"hgvs_p": "p.Arg225Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861270.1",
"strand": false,
"transcript": "XM_017005781.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 481,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2143,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 1446,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011533420.2",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531722.1",
"strand": false,
"transcript": "XM_011533420.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 469,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1978,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011533421.3",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531723.1",
"strand": false,
"transcript": "XM_011533421.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 463,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1578,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 1392,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005264899.5",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Arg445Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005264956.1",
"strand": false,
"transcript": "XM_005264899.5",
"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": 6754,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XR_940385.1",
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"hgvs_c": "n.1418G>A",
"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": "XR_940385.1",
"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": 2051,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000418161.2",
"gene_hgnc_id": 41142,
"gene_symbol": "CCDC13-AS1",
"hgvs_c": "n.84+3086C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000418161.2",
"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": 554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000446950.5",
"gene_hgnc_id": 41142,
"gene_symbol": "CCDC13-AS1",
"hgvs_c": "n.84+3086C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000446950.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1128,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000665649.1",
"gene_hgnc_id": 41142,
"gene_symbol": "CCDC13-AS1",
"hgvs_c": "n.84+3086C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000665649.1",
"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": 554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_046732.1",
"gene_hgnc_id": 41142,
"gene_symbol": "CCDC13-AS1",
"hgvs_c": "n.84+3086C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_046732.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs956450866",
"effect": "missense_variant",
"frequency_reference_population": 0.000005472443,
"gene_hgnc_id": 26358,
"gene_symbol": "CCDC13",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000547244,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.337,
"pos": 42735744,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.061,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_144719.4"
}
]
}