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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: 3-38008094-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38008094&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38008094,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001130964.2",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2105T>C",
"hgvs_p": "p.Phe702Ser",
"transcript": "NM_006225.4",
"protein_id": "NP_006216.2",
"transcript_support_level": null,
"aa_start": 702,
"aa_end": null,
"aa_length": 756,
"cds_start": 2105,
"cds_end": null,
"cds_length": 2271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000334661.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006225.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2105T>C",
"hgvs_p": "p.Phe702Ser",
"transcript": "ENST00000334661.5",
"protein_id": "ENSP00000335600.4",
"transcript_support_level": 1,
"aa_start": 702,
"aa_end": null,
"aa_length": 756,
"cds_start": 2105,
"cds_end": null,
"cds_length": 2271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006225.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334661.5"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2168T>C",
"hgvs_p": "p.Phe723Ser",
"transcript": "NM_001130964.2",
"protein_id": "NP_001124436.1",
"transcript_support_level": null,
"aa_start": 723,
"aa_end": null,
"aa_length": 777,
"cds_start": 2168,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130964.2"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2168T>C",
"hgvs_p": "p.Phe723Ser",
"transcript": "ENST00000463876.5",
"protein_id": "ENSP00000430344.1",
"transcript_support_level": 2,
"aa_start": 723,
"aa_end": null,
"aa_length": 777,
"cds_start": 2168,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000463876.5"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2102T>C",
"hgvs_p": "p.Phe701Ser",
"transcript": "ENST00000956065.1",
"protein_id": "ENSP00000626124.1",
"transcript_support_level": null,
"aa_start": 701,
"aa_end": null,
"aa_length": 755,
"cds_start": 2102,
"cds_end": null,
"cds_length": 2268,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956065.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2087T>C",
"hgvs_p": "p.Phe696Ser",
"transcript": "ENST00000909334.1",
"protein_id": "ENSP00000579393.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 750,
"cds_start": 2087,
"cds_end": null,
"cds_length": 2253,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909334.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2063T>C",
"hgvs_p": "p.Phe688Ser",
"transcript": "ENST00000909335.1",
"protein_id": "ENSP00000579394.1",
"transcript_support_level": null,
"aa_start": 688,
"aa_end": null,
"aa_length": 742,
"cds_start": 2063,
"cds_end": null,
"cds_length": 2229,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909335.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.1988T>C",
"hgvs_p": "p.Phe663Ser",
"transcript": "ENST00000937408.1",
"protein_id": "ENSP00000607467.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 717,
"cds_start": 1988,
"cds_end": null,
"cds_length": 2154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937408.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.1955T>C",
"hgvs_p": "p.Phe652Ser",
"transcript": "ENST00000909333.1",
"protein_id": "ENSP00000579392.1",
"transcript_support_level": null,
"aa_start": 652,
"aa_end": null,
"aa_length": 706,
"cds_start": 1955,
"cds_end": null,
"cds_length": 2121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909333.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.1940T>C",
"hgvs_p": "p.Phe647Ser",
"transcript": "ENST00000909336.1",
"protein_id": "ENSP00000579395.1",
"transcript_support_level": null,
"aa_start": 647,
"aa_end": null,
"aa_length": 701,
"cds_start": 1940,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909336.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.1772T>C",
"hgvs_p": "p.Phe591Ser",
"transcript": "ENST00000956063.1",
"protein_id": "ENSP00000626122.1",
"transcript_support_level": null,
"aa_start": 591,
"aa_end": null,
"aa_length": 645,
"cds_start": 1772,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956063.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.2036-12T>C",
"hgvs_p": null,
"transcript": "ENST00000909332.1",
"protein_id": "ENSP00000579391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 729,
"cds_start": null,
"cds_end": null,
"cds_length": 2190,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909332.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "c.1886-12T>C",
"hgvs_p": null,
"transcript": "ENST00000956064.1",
"protein_id": "ENSP00000626123.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 679,
"cds_start": null,
"cds_end": null,
"cds_length": 2040,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956064.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "n.242T>C",
"hgvs_p": null,
"transcript": "ENST00000417185.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000417185.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "n.2828T>C",
"hgvs_p": null,
"transcript": "ENST00000461445.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461445.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "n.2332T>C",
"hgvs_p": null,
"transcript": "NR_024071.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_024071.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"hgvs_c": "n.*180T>C",
"hgvs_p": null,
"transcript": "ENST00000495395.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000495395.1"
}
],
"gene_symbol": "PLCD1",
"gene_hgnc_id": 9060,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9742065668106079,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.712,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.269,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001130964.2",
"gene_symbol": "PLCD1",
"hgnc_id": 9060,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2168T>C",
"hgvs_p": "p.Phe723Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}