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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: 2-86986628-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86986628&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RGPD1",
"hgnc_id": 32414,
"hgvs_c": "c.3729C>G",
"hgvs_p": "p.Asn1243Lys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_001382344.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": null,
"alphamissense_prediction": null,
"alphamissense_score": 0.2552,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "2",
"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": 0.2020852267742157,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1756,
"aa_ref": "N",
"aa_start": 1243,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6819,
"cdna_start": 3848,
"cds_end": null,
"cds_length": 5271,
"cds_start": 3729,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001382344.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3729C>G",
"hgvs_p": "p.Asn1243Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000641458.2",
"protein_coding": true,
"protein_id": "NP_001369273.1",
"strand": true,
"transcript": "NM_001382344.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1756,
"aa_ref": "N",
"aa_start": 1243,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6819,
"cdna_start": 3848,
"cds_end": null,
"cds_length": 5271,
"cds_start": 3729,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000641458.2",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3729C>G",
"hgvs_p": "p.Asn1243Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001382344.1",
"protein_coding": true,
"protein_id": "ENSP00000492954.1",
"strand": true,
"transcript": "ENST00000641458.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1756,
"aa_ref": "N",
"aa_start": 1243,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5425,
"cdna_start": 3767,
"cds_end": null,
"cds_length": 5271,
"cds_start": 3729,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000398193.8",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3729C>G",
"hgvs_p": "p.Asn1243Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381253.3",
"strand": true,
"transcript": "ENST00000398193.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3479,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000428128.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "n.*1648C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000402729.1",
"strand": true,
"transcript": "ENST00000428128.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3479,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000428128.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "n.*1648C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000402729.1",
"strand": true,
"transcript": "ENST00000428128.1",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1756,
"aa_ref": "N",
"aa_start": 1243,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6891,
"cdna_start": 3920,
"cds_end": null,
"cds_length": 5271,
"cds_start": 3729,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001410915.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3729C>G",
"hgvs_p": "p.Asn1243Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397844.1",
"strand": true,
"transcript": "NM_001410915.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1748,
"aa_ref": "N",
"aa_start": 1235,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6692,
"cdna_start": 3721,
"cds_end": null,
"cds_length": 5247,
"cds_start": 3705,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001024457.4",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3705C>G",
"hgvs_p": "p.Asn1235Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001019628.3",
"strand": true,
"transcript": "NM_001024457.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1801,
"aa_ref": "N",
"aa_start": 1288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6907,
"cdna_start": 3936,
"cds_end": null,
"cds_length": 5406,
"cds_start": 3864,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011532845.4",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3864C>G",
"hgvs_p": "p.Asn1288Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531147.1",
"strand": true,
"transcript": "XM_011532845.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1696,
"aa_ref": "N",
"aa_start": 1260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5915,
"cdna_start": 3796,
"cds_end": null,
"cds_length": 5091,
"cds_start": 3780,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011532849.4",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3780C>G",
"hgvs_p": "p.Asn1260Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531151.2",
"strand": true,
"transcript": "XM_011532849.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1684,
"aa_ref": "N",
"aa_start": 1260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7058,
"cdna_start": 3796,
"cds_end": null,
"cds_length": 5055,
"cds_start": 3780,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011532850.3",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3780C>G",
"hgvs_p": "p.Asn1260Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531152.2",
"strand": true,
"transcript": "XM_011532850.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1670,
"aa_ref": "N",
"aa_start": 1260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5837,
"cdna_start": 3796,
"cds_end": null,
"cds_length": 5013,
"cds_start": 3780,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011532851.4",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3780C>G",
"hgvs_p": "p.Asn1260Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531153.2",
"strand": true,
"transcript": "XM_011532851.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1669,
"aa_ref": "N",
"aa_start": 1260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5093,
"cdna_start": 3796,
"cds_end": null,
"cds_length": 5010,
"cds_start": 3780,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011532852.4",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "c.3780C>G",
"hgvs_p": "p.Asn1260Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531154.2",
"strand": true,
"transcript": "XM_011532852.4",
"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": 5271,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XR_007074605.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "n.3796C>G",
"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": "XR_007074605.1",
"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": 5226,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XR_007074622.1",
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"hgvs_c": "n.3796C>G",
"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": "XR_007074622.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1280697105",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 32414,
"gene_symbol": "RGPD1",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000384533,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 0,
"gnomad_genomes_af": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": null,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.634,
"pos": 86986628,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.118,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001382344.1"
}
]
}