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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: 1-63623761-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=63623761&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"PVS1",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "PGM1",
"hgnc_id": 8905,
"hgvs_c": "c.300+1G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 8,
"score": -8,
"transcript": "NM_001172818.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PVS1,BP6_Very_Strong,BS1,BS2",
"acmg_score": -8,
"allele_count_reference_population": 20085,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"chr": "1",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "PGM1-congenital disorder of glycosylation,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 562,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2337,
"cdna_start": null,
"cds_end": null,
"cds_length": 1689,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002633.3",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371084.8",
"protein_coding": true,
"protein_id": "NP_002624.2",
"strand": true,
"transcript": "NM_002633.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 562,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2337,
"cdna_start": null,
"cds_end": null,
"cds_length": 1689,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000371084.8",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002633.3",
"protein_coding": true,
"protein_id": "ENSP00000360125.3",
"strand": true,
"transcript": "ENST00000371084.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 594,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2555,
"cdna_start": null,
"cds_end": null,
"cds_length": 1785,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000895883.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565942.1",
"strand": true,
"transcript": "ENST00000895883.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 584,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2423,
"cdna_start": null,
"cds_end": null,
"cds_length": 1755,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650546.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497812.1",
"strand": true,
"transcript": "ENST00000650546.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2558,
"cdna_start": null,
"cds_end": null,
"cds_length": 1743,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001172818.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.300+1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166289.1",
"strand": true,
"transcript": "NM_001172818.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2657,
"cdna_start": null,
"cds_end": null,
"cds_length": 1743,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000371083.4",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.300+1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000360124.4",
"strand": true,
"transcript": "ENST00000371083.4",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 579,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2427,
"cdna_start": null,
"cds_end": null,
"cds_length": 1740,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000895884.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565943.1",
"strand": true,
"transcript": "ENST00000895884.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 574,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2384,
"cdna_start": null,
"cds_end": null,
"cds_length": 1725,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966605.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636664.1",
"strand": true,
"transcript": "ENST00000966605.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 568,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2525,
"cdna_start": null,
"cds_end": null,
"cds_length": 1707,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000895882.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565941.1",
"strand": true,
"transcript": "ENST00000895882.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 559,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2443,
"cdna_start": null,
"cds_end": null,
"cds_length": 1680,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000925889.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595948.1",
"strand": true,
"transcript": "ENST00000925889.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 478,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2081,
"cdna_start": null,
"cds_end": null,
"cds_length": 1437,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966606.1",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.247-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636665.1",
"strand": true,
"transcript": "ENST00000966606.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2349,
"cdna_start": null,
"cds_end": null,
"cds_length": 1098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001172819.2",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.-345-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166290.1",
"strand": true,
"transcript": "NM_001172819.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2345,
"cdna_start": null,
"cds_end": null,
"cds_length": 1098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000540265.5",
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"hgvs_c": "c.-345-5664G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443449.1",
"strand": true,
"transcript": "ENST00000540265.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999984967332678,
"dbsnp": "rs77043134",
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": 0.012537046,
"gene_hgnc_id": 8905,
"gene_symbol": "PGM1",
"gnomad_exomes_ac": 18533,
"gnomad_exomes_af": 0.0127832,
"gnomad_exomes_homalt": 132,
"gnomad_genomes_ac": 1552,
"gnomad_genomes_af": 0.010193,
"gnomad_genomes_homalt": 24,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 156,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not provided|PGM1-congenital disorder of glycosylation",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.556,
"pos": 63623761,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9399999976158142,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001172818.1"
}
]
}