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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: 19-7542043-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7542043&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"inheritance_mode": "AR",
"pathogenic_score": 1,
"score": -3,
"transcript": "NM_001166111.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Strong",
"acmg_score": -3,
"allele_count_reference_population": 115,
"alphamissense_prediction": null,
"alphamissense_score": 0.0555,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "19",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Hereditary spastic paraplegia 39,Inborn genetic diseases,Laurence-Moon syndrome,Trichomegaly-retina pigmentary degeneration-dwarfism syndrome,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04119902849197388,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "V",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 1300,
"cds_end": null,
"cds_length": 4098,
"cds_start": 1228,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001166114.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1228G>A",
"hgvs_p": "p.Val410Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000600737.6",
"protein_coding": true,
"protein_id": "NP_001159586.1",
"strand": true,
"transcript": "NM_001166114.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "V",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 1300,
"cds_end": null,
"cds_length": 4098,
"cds_start": 1228,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000600737.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1228G>A",
"hgvs_p": "p.Val410Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001166114.2",
"protein_coding": true,
"protein_id": "ENSP00000473211.1",
"strand": true,
"transcript": "ENST00000600737.6",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4617,
"cdna_start": 1542,
"cds_end": null,
"cds_length": 3984,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000221249.10",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000221249.5",
"strand": true,
"transcript": "ENST00000221249.10",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 3984,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000450331.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394348.2",
"strand": true,
"transcript": "ENST00000450331.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "V",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4536,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 4128,
"cds_start": 1255,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001166111.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159583.1",
"strand": true,
"transcript": "NM_001166111.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "V",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4522,
"cdna_start": 1450,
"cds_end": null,
"cds_length": 4128,
"cds_start": 1255,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000414982.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000407509.2",
"strand": true,
"transcript": "ENST00000414982.7",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4460,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 3984,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001166113.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159585.1",
"strand": true,
"transcript": "NM_001166113.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 3984,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_006702.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_006693.3",
"strand": true,
"transcript": "NM_006702.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4505,
"cdna_start": 1511,
"cds_end": null,
"cds_length": 3903,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001166112.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159584.1",
"strand": true,
"transcript": "NM_001166112.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "V",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4502,
"cdna_start": 1511,
"cds_end": null,
"cds_length": 3903,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000545201.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.1111G>A",
"hgvs_p": "p.Val371Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443323.1",
"strand": true,
"transcript": "ENST00000545201.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 265,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 800,
"cdna_start": null,
"cds_end": null,
"cds_length": 798,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000595264.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.688+359G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472456.1",
"strand": true,
"transcript": "ENST00000595264.5",
"transcript_support_level": 3
},
{
"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": 999,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000595176.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "n.297G>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": "ENST00000595176.5",
"transcript_support_level": 3
},
{
"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": 1005,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000599311.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "n.263G>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": "ENST00000599311.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs369465821",
"effect": "missense_variant",
"frequency_reference_population": 0.00007155738,
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"gnomad_exomes_ac": 105,
"gnomad_exomes_af": 0.0000721755,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.0000656538,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Hereditary spastic paraplegia 39|Inborn genetic diseases|Hereditary spastic paraplegia 39;Trichomegaly-retina pigmentary degeneration-dwarfism syndrome;Laurence-Moon syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.901,
"pos": 7542043,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.073,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001166111.2"
}
]
}