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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: 19-44647349-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=44647349&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PVR",
"hgnc_id": 9705,
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_006505.5",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CEACAM16-AS1",
"hgnc_id": 55317,
"hgvs_c": "n.476-14730T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000662585.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.0867,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"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": 0.03675559163093567,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 417,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5792,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1254,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_006505.5",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000425690.8",
"protein_coding": true,
"protein_id": "NP_006496.4",
"strand": true,
"transcript": "NM_006505.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 417,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5792,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1254,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000425690.8",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006505.5",
"protein_coding": true,
"protein_id": "ENSP00000402060.2",
"strand": true,
"transcript": "ENST00000425690.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 392,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1344,
"cdna_start": 206,
"cds_end": null,
"cds_length": 1179,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000406449.8",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000383907.3",
"strand": true,
"transcript": "ENST00000406449.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 444,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3322,
"cdna_start": 422,
"cds_end": null,
"cds_length": 1335,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000971445.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641504.1",
"strand": true,
"transcript": "ENST00000971445.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 439,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3398,
"cdna_start": 483,
"cds_end": null,
"cds_length": 1320,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000706603.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516465.1",
"strand": true,
"transcript": "ENST00000706603.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 424,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3311,
"cdna_start": 470,
"cds_end": null,
"cds_length": 1275,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000937736.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607795.1",
"strand": true,
"transcript": "ENST00000937736.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 392,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1531,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1179,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001135770.4",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001129242.2",
"strand": true,
"transcript": "NM_001135770.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 372,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5657,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1119,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001135768.3",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001129240.1",
"strand": true,
"transcript": "NM_001135768.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 372,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3078,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1119,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000403059.8",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385344.3",
"strand": true,
"transcript": "ENST00000403059.8",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 368,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3140,
"cdna_start": 470,
"cds_end": null,
"cds_length": 1107,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000971444.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641503.1",
"strand": true,
"transcript": "ENST00000971444.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 364,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5633,
"cdna_start": 393,
"cds_end": null,
"cds_length": 1095,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001135769.3",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001129241.1",
"strand": true,
"transcript": "NM_001135769.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 364,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3166,
"cdna_start": 505,
"cds_end": null,
"cds_length": 1095,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000344956.8",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000340870.3",
"strand": true,
"transcript": "ENST00000344956.8",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 335,
"aa_ref": "H",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2165,
"cdna_start": 431,
"cds_end": null,
"cds_length": 1008,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000706606.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "c.206A>T",
"hgvs_p": "p.His69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516467.1",
"strand": true,
"transcript": "ENST00000706606.1",
"transcript_support_level": null
},
{
"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": 3132,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000187830.2",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "n.129A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000187830.2",
"strand": true,
"transcript": "ENST00000187830.2",
"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": 4743,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000706604.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "n.206A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000516466.1",
"strand": true,
"transcript": "ENST00000706604.1",
"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": 6466,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000706605.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "n.445A>T",
"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": "ENST00000706605.1",
"transcript_support_level": null
},
{
"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": 3087,
"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": "ENST00000706607.1",
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"hgvs_c": "n.206A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000516468.1",
"strand": true,
"transcript": "ENST00000706607.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 829,
"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": "ENST00000590796.1",
"gene_hgnc_id": 55317,
"gene_symbol": "CEACAM16-AS1",
"hgvs_c": "n.409-14730T>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590796.1",
"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": 1522,
"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": "ENST00000662585.1",
"gene_hgnc_id": 55317,
"gene_symbol": "CEACAM16-AS1",
"hgvs_c": "n.476-14730T>A",
"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": "ENST00000662585.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs539060105",
"effect": "missense_variant",
"frequency_reference_population": 0.0000018592107,
"gene_hgnc_id": 9705,
"gene_symbol": "PVR",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84229e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131501,
"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": -3.049,
"pos": 44647349,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.284,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006505.5"
}
]
}