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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: 19-43018821-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=43018821&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PSG11",
"hgnc_id": 9516,
"hgvs_c": "c.658T>G",
"hgvs_p": "p.Trp220Gly",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_002785.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PSG11-AS1",
"hgnc_id": 56358,
"hgvs_c": "n.182+41177A>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000635495.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.0963,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.76,
"chr": "19",
"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": 0.08735707402229309,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 335,
"aa_ref": "W",
"aa_start": 220,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1532,
"cdna_start": 755,
"cds_end": null,
"cds_length": 1008,
"cds_start": 658,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002785.3",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.658T>G",
"hgvs_p": "p.Trp220Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000320078.12",
"protein_coding": true,
"protein_id": "NP_002776.3",
"strand": false,
"transcript": "NM_002785.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 335,
"aa_ref": "W",
"aa_start": 220,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1532,
"cdna_start": 755,
"cds_end": null,
"cds_length": 1008,
"cds_start": 658,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000320078.12",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.658T>G",
"hgvs_p": "p.Trp220Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002785.3",
"protein_coding": true,
"protein_id": "ENSP00000319140.7",
"strand": false,
"transcript": "ENST00000320078.12",
"transcript_support_level": 2
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 213,
"aa_ref": "W",
"aa_start": 98,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 990,
"cdna_start": 389,
"cds_end": null,
"cds_length": 642,
"cds_start": 292,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000306322.7",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.292T>G",
"hgvs_p": "p.Trp98Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000304913.6",
"strand": false,
"transcript": "ENST00000306322.7",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 213,
"aa_ref": "W",
"aa_start": 98,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1166,
"cdna_start": 389,
"cds_end": null,
"cds_length": 642,
"cds_start": 292,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001113410.2",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.292T>G",
"hgvs_p": "p.Trp98Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001106881.1",
"strand": false,
"transcript": "NM_001113410.2",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 213,
"aa_ref": "W",
"aa_start": 98,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1234,
"cdna_start": 389,
"cds_end": null,
"cds_length": 642,
"cds_start": 292,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_203287.2",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.292T>G",
"hgvs_p": "p.Trp98Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_976032.2",
"strand": false,
"transcript": "NM_203287.2",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 213,
"aa_ref": "W",
"aa_start": 98,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1163,
"cdna_start": 386,
"cds_end": null,
"cds_length": 642,
"cds_start": 292,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000403486.5",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.292T>G",
"hgvs_p": "p.Trp98Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385427.1",
"strand": false,
"transcript": "ENST00000403486.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 335,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1084,
"cdna_start": null,
"cds_end": null,
"cds_length": 1008,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000598133.2",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "c.431-2776T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472372.2",
"strand": false,
"transcript": "ENST00000598133.2",
"transcript_support_level": 5
},
{
"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": 527,
"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": "ENST00000488205.1",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.394T>G",
"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": "ENST00000488205.1",
"transcript_support_level": 5
},
{
"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": 1942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000593983.5",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.*509T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000472717.1",
"strand": false,
"transcript": "ENST00000593983.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 649,
"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": "ENST00000595312.1",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.227T>G",
"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": "ENST00000595312.1",
"transcript_support_level": 5
},
{
"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": 861,
"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": "ENST00000597093.1",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.382T>G",
"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": "ENST00000597093.1",
"transcript_support_level": 2
},
{
"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": 1942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000593983.5",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.*509T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000472717.1",
"strand": false,
"transcript": "ENST00000593983.5",
"transcript_support_level": 5
},
{
"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": 1810,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000594655.5",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.521-3451T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000594655.5",
"transcript_support_level": 5
},
{
"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": 1916,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000595138.1",
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"hgvs_c": "n.521-2776T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000595138.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1833,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635495.1",
"gene_hgnc_id": 56358,
"gene_symbol": "PSG11-AS1",
"hgvs_c": "n.182+41177A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000635495.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs575017081",
"effect": "missense_variant",
"frequency_reference_population": 6.846642e-7,
"gene_hgnc_id": 9516,
"gene_symbol": "PSG11",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84664e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": -4.91,
"pos": 43018821,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.016,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002785.3"
}
]
}