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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: 3-149009277-TG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149009277&ref=TG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PS3",
"PP5_Very_Strong"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "GYG1",
"hgnc_id": 4699,
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"inheritance_mode": "AR",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_004130.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 659,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "3",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Glycogen storage disease XV,Polyglucosan body myopathy type 2,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 350,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5996,
"cdna_start": 588,
"cds_end": null,
"cds_length": 1053,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_004130.4",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000345003.9",
"protein_coding": true,
"protein_id": "NP_004121.2",
"strand": true,
"transcript": "NM_004130.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 350,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5996,
"cdna_start": 588,
"cds_end": null,
"cds_length": 1053,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000345003.9",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004130.4",
"protein_coding": true,
"protein_id": "ENSP00000340736.4",
"strand": true,
"transcript": "ENST00000345003.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 333,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1890,
"cdna_start": 676,
"cds_end": null,
"cds_length": 1002,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000296048.10",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000296048.6",
"strand": true,
"transcript": "ENST00000296048.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 279,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1563,
"cdna_start": 570,
"cds_end": null,
"cds_length": 840,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000484197.5",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420683.1",
"strand": true,
"transcript": "ENST00000484197.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 372,
"aa_ref": "D",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1917,
"cdna_start": 653,
"cds_end": null,
"cds_length": 1119,
"cds_start": 553,
"consequences": [
"frameshift_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000942926.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.553delG",
"hgvs_p": "p.Asp185fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612985.1",
"strand": true,
"transcript": "ENST00000942926.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 355,
"aa_ref": "D",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1871,
"cdna_start": 657,
"cds_end": null,
"cds_length": 1068,
"cds_start": 553,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000852398.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.553delG",
"hgvs_p": "p.Asp185fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522457.1",
"strand": true,
"transcript": "ENST00000852398.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 333,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5945,
"cdna_start": 588,
"cds_end": null,
"cds_length": 1002,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001184720.2",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171649.1",
"strand": true,
"transcript": "NM_001184720.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 332,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1841,
"cdna_start": 630,
"cds_end": null,
"cds_length": 999,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000852397.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522456.1",
"strand": true,
"transcript": "ENST00000852397.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 279,
"aa_ref": "D",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5725,
"cdna_start": 588,
"cds_end": null,
"cds_length": 840,
"cds_start": 487,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001184721.2",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.487delG",
"hgvs_p": "p.Asp163fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171650.1",
"strand": true,
"transcript": "NM_001184721.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 264,
"aa_ref": "D",
"aa_start": 159,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 866,
"cdna_start": 544,
"cds_end": null,
"cds_length": 797,
"cds_start": 475,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000461191.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.475delG",
"hgvs_p": "p.Asp159fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420247.1",
"strand": true,
"transcript": "ENST00000461191.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 264,
"aa_ref": "D",
"aa_start": 94,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1534,
"cdna_start": 321,
"cds_end": null,
"cds_length": 795,
"cds_start": 280,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000942927.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.280delG",
"hgvs_p": "p.Asp94fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612986.1",
"strand": true,
"transcript": "ENST00000942927.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 175,
"aa_ref": "D",
"aa_start": 5,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1481,
"cdna_start": 231,
"cds_end": null,
"cds_length": 528,
"cds_start": 13,
"consequences": [
"frameshift_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000942925.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.13delG",
"hgvs_p": "p.Asp5fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612984.1",
"strand": true,
"transcript": "ENST00000942925.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5809,
"cdna_start": 452,
"cds_end": null,
"cds_length": 825,
"cds_start": 310,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017006275.2",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.310delG",
"hgvs_p": "p.Asp104fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861764.1",
"strand": true,
"transcript": "XM_017006275.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 179,
"aa_ref": "D",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6356,
"cdna_start": 999,
"cds_end": null,
"cds_length": 540,
"cds_start": 25,
"consequences": [
"frameshift_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017006276.2",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.25delG",
"hgvs_p": "p.Asp9fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861765.1",
"strand": true,
"transcript": "XM_017006276.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 193,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1831,
"cdna_start": null,
"cds_end": null,
"cds_length": 582,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000627418.2",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "c.469+12389delG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486061.1",
"strand": true,
"transcript": "ENST00000627418.2",
"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": 704,
"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": "ENST00000469873.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "n.401delG",
"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": "ENST00000469873.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 812,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000479119.1",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "n.103delG",
"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": "ENST00000479119.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 234,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000497528.5",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "n.126delG",
"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": "ENST00000497528.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 801,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000483267.6",
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"hgvs_c": "n.598+12389delG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483267.6",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs727502871",
"effect": "frameshift_variant",
"frequency_reference_population": 0.00040906676,
"gene_hgnc_id": 4699,
"gene_symbol": "GYG1",
"gnomad_exomes_ac": 595,
"gnomad_exomes_af": 0.000407901,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 64,
"gnomad_genomes_af": 0.000420234,
"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": "Pathogenic",
"phenotype_combined": "Polyglucosan body myopathy type 2|not provided|Glycogen storage disease XV|Glycogen storage disease XV;Polyglucosan body myopathy type 2",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"pos": 149009277,
"ref": "TG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_004130.4"
}
]
}