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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: 19-7556507-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7556507&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7556507,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001166111.2",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3148A>G",
"hgvs_p": "p.Met1050Val",
"transcript": "NM_001166114.2",
"protein_id": "NP_001159586.1",
"transcript_support_level": null,
"aa_start": 1050,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3148,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000600737.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166114.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3148A>G",
"hgvs_p": "p.Met1050Val",
"transcript": "ENST00000600737.6",
"protein_id": "ENSP00000473211.1",
"transcript_support_level": 1,
"aa_start": 1050,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3148,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001166114.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600737.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3034A>G",
"hgvs_p": "p.Met1012Val",
"transcript": "ENST00000221249.10",
"protein_id": "ENSP00000221249.5",
"transcript_support_level": 1,
"aa_start": 1012,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3034,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000221249.10"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3034A>G",
"hgvs_p": "p.Met1012Val",
"transcript": "ENST00000450331.7",
"protein_id": "ENSP00000394348.2",
"transcript_support_level": 1,
"aa_start": 1012,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3034,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450331.7"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3178A>G",
"hgvs_p": "p.Met1060Val",
"transcript": "NM_001166111.2",
"protein_id": "NP_001159583.1",
"transcript_support_level": null,
"aa_start": 1060,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3178,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166111.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3178A>G",
"hgvs_p": "p.Met1060Val",
"transcript": "ENST00000414982.7",
"protein_id": "ENSP00000407509.2",
"transcript_support_level": 2,
"aa_start": 1060,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3178,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414982.7"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3034A>G",
"hgvs_p": "p.Met1012Val",
"transcript": "NM_001166113.1",
"protein_id": "NP_001159585.1",
"transcript_support_level": null,
"aa_start": 1012,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3034,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166113.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3034A>G",
"hgvs_p": "p.Met1012Val",
"transcript": "NM_006702.5",
"protein_id": "NP_006693.3",
"transcript_support_level": null,
"aa_start": 1012,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3034,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006702.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2953A>G",
"hgvs_p": "p.Met985Val",
"transcript": "NM_001166112.2",
"protein_id": "NP_001159584.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2953,
"cds_end": null,
"cds_length": 3903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166112.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2953A>G",
"hgvs_p": "p.Met985Val",
"transcript": "ENST00000545201.6",
"protein_id": "ENSP00000443323.1",
"transcript_support_level": 2,
"aa_start": 985,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2953,
"cds_end": null,
"cds_length": 3903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000545201.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Met107Val",
"transcript": "ENST00000646984.1",
"protein_id": "ENSP00000496219.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 223,
"cds_start": 319,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646984.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "n.-7A>G",
"hgvs_p": null,
"transcript": "ENST00000595352.1",
"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": "ENST00000595352.1"
}
],
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"dbsnp": "rs121434415",
"frequency_reference_population": 0.000003098569,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273652,
"gnomad_genomes_af": 0.00000658172,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8902081251144409,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.854,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.244,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.301,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001166111.2",
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3178A>G",
"hgvs_p": "p.Met1060Val"
}
],
"clinvar_disease": "Ataxia-hypogonadism-choroidal dystrophy syndrome,Hereditary spastic paraplegia 39",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Hereditary spastic paraplegia 39|Ataxia-hypogonadism-choroidal dystrophy syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}