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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: 3-38008283-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38008283&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "PLCD1",
"hgnc_id": 9060,
"hgvs_c": "c.2050G>A",
"hgvs_p": "p.Val684Met",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001130964.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 58,
"alphamissense_prediction": null,
"alphamissense_score": 0.3193,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.08,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5303130149841309,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 756,
"aa_ref": "V",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": 2090,
"cds_end": null,
"cds_length": 2271,
"cds_start": 1987,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_006225.4",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Val663Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000334661.5",
"protein_coding": true,
"protein_id": "NP_006216.2",
"strand": false,
"transcript": "NM_006225.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 756,
"aa_ref": "V",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": 2090,
"cds_end": null,
"cds_length": 2271,
"cds_start": 1987,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000334661.5",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Val663Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006225.4",
"protein_coding": true,
"protein_id": "ENSP00000335600.4",
"strand": false,
"transcript": "ENST00000334661.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 777,
"aa_ref": "V",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2698,
"cdna_start": 2137,
"cds_end": null,
"cds_length": 2334,
"cds_start": 2050,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001130964.2",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.2050G>A",
"hgvs_p": "p.Val684Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001124436.1",
"strand": false,
"transcript": "NM_001130964.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 777,
"aa_ref": "V",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2963,
"cdna_start": 2404,
"cds_end": null,
"cds_length": 2334,
"cds_start": 2050,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000463876.5",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.2050G>A",
"hgvs_p": "p.Val684Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000430344.1",
"strand": false,
"transcript": "ENST00000463876.5",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 755,
"aa_ref": "V",
"aa_start": 662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2644,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 2268,
"cds_start": 1984,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000956065.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1984G>A",
"hgvs_p": "p.Val662Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626124.1",
"strand": false,
"transcript": "ENST00000956065.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 750,
"aa_ref": "V",
"aa_start": 657,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2633,
"cdna_start": 2072,
"cds_end": null,
"cds_length": 2253,
"cds_start": 1969,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000909334.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1969G>A",
"hgvs_p": "p.Val657Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579393.1",
"strand": false,
"transcript": "ENST00000909334.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 742,
"aa_ref": "V",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2607,
"cdna_start": 2090,
"cds_end": null,
"cds_length": 2229,
"cds_start": 1987,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000909335.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Val663Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579394.1",
"strand": false,
"transcript": "ENST00000909335.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 729,
"aa_ref": "V",
"aa_start": 663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2575,
"cdna_start": 2095,
"cds_end": null,
"cds_length": 2190,
"cds_start": 1987,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000909332.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Val663Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579391.1",
"strand": false,
"transcript": "ENST00000909332.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 717,
"aa_ref": "V",
"aa_start": 624,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2533,
"cdna_start": 1975,
"cds_end": null,
"cds_length": 2154,
"cds_start": 1870,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000937408.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1870G>A",
"hgvs_p": "p.Val624Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607467.1",
"strand": false,
"transcript": "ENST00000937408.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 706,
"aa_ref": "V",
"aa_start": 613,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2502,
"cdna_start": 1941,
"cds_end": null,
"cds_length": 2121,
"cds_start": 1837,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909333.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1837G>A",
"hgvs_p": "p.Val613Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579392.1",
"strand": false,
"transcript": "ENST00000909333.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 701,
"aa_ref": "V",
"aa_start": 608,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2482,
"cdna_start": 1925,
"cds_end": null,
"cds_length": 2106,
"cds_start": 1822,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909336.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1822G>A",
"hgvs_p": "p.Val608Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579395.1",
"strand": false,
"transcript": "ENST00000909336.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 679,
"aa_ref": "V",
"aa_start": 613,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2417,
"cdna_start": 1945,
"cds_end": null,
"cds_length": 2040,
"cds_start": 1837,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000956064.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1837G>A",
"hgvs_p": "p.Val613Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626123.1",
"strand": false,
"transcript": "ENST00000956064.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 645,
"aa_ref": "V",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2347,
"cdna_start": 1790,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1654,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000956063.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "c.1654G>A",
"hgvs_p": "p.Val552Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626122.1",
"strand": false,
"transcript": "ENST00000956063.1",
"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": 685,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000417185.6",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "n.53G>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": "ENST00000417185.6",
"transcript_support_level": 2
},
{
"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": 3271,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000461445.5",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "n.2710G>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": "ENST00000461445.5",
"transcript_support_level": 2
},
{
"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": 401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000495395.1",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "n.392G>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": "ENST00000495395.1",
"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": 2775,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NR_024071.2",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "n.2214G>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": "NR_024071.2",
"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": 1044,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000484829.5",
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"hgvs_c": "n.*180G>A",
"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": "ENST00000484829.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs78426951",
"effect": "missense_variant",
"frequency_reference_population": 0.000035930356,
"gene_hgnc_id": 9060,
"gene_symbol": "PLCD1",
"gnomad_exomes_ac": 53,
"gnomad_exomes_af": 0.0000362551,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328144,
"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": "Benign",
"phylop100way_score": 2.728,
"pos": 38008283,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.391,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001130964.2"
}
]
}