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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: 19-48977986-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48977986&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48977986,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002103.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1246A>G",
"hgvs_p": "p.Met416Val",
"transcript": "NM_002103.5",
"protein_id": "NP_002094.2",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 737,
"cds_start": 1246,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000323798.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002103.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1246A>G",
"hgvs_p": "p.Met416Val",
"transcript": "ENST00000323798.8",
"protein_id": "ENSP00000317904.3",
"transcript_support_level": 1,
"aa_start": 416,
"aa_end": null,
"aa_length": 737,
"cds_start": 1246,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002103.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323798.8"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1054A>G",
"hgvs_p": "p.Met352Val",
"transcript": "ENST00000263276.6",
"protein_id": "ENSP00000263276.6",
"transcript_support_level": 1,
"aa_start": 352,
"aa_end": null,
"aa_length": 673,
"cds_start": 1054,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263276.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1312A>G",
"hgvs_p": "p.Met438Val",
"transcript": "ENST00000960032.1",
"protein_id": "ENSP00000630091.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 759,
"cds_start": 1312,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960032.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1270A>G",
"hgvs_p": "p.Met424Val",
"transcript": "ENST00000960031.1",
"protein_id": "ENSP00000630090.1",
"transcript_support_level": null,
"aa_start": 424,
"aa_end": null,
"aa_length": 745,
"cds_start": 1270,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960031.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1102A>G",
"hgvs_p": "p.Met368Val",
"transcript": "ENST00000960033.1",
"protein_id": "ENSP00000630092.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 689,
"cds_start": 1102,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960033.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1060A>G",
"hgvs_p": "p.Met354Val",
"transcript": "ENST00000917526.1",
"protein_id": "ENSP00000587585.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 675,
"cds_start": 1060,
"cds_end": null,
"cds_length": 2028,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917526.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1054A>G",
"hgvs_p": "p.Met352Val",
"transcript": "NM_001161587.2",
"protein_id": "NP_001155059.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 673,
"cds_start": 1054,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001161587.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.484A>G",
"hgvs_p": "p.Met162Val",
"transcript": "ENST00000917525.1",
"protein_id": "ENSP00000587584.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 483,
"cds_start": 484,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917525.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000472004.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000472004.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "n.153A>G",
"hgvs_p": null,
"transcript": "ENST00000496048.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000496048.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "n.1261A>G",
"hgvs_p": null,
"transcript": "NR_027763.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027763.2"
}
],
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"dbsnp": "rs5447",
"frequency_reference_population": 0.009692513,
"hom_count_reference_population": 426,
"allele_count_reference_population": 15643,
"gnomad_exomes_af": 0.00915193,
"gnomad_genomes_af": 0.0148858,
"gnomad_exomes_ac": 13378,
"gnomad_genomes_ac": 2265,
"gnomad_exomes_homalt": 359,
"gnomad_genomes_homalt": 67,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0027920901775360107,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": 0.0648,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.347,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002103.5",
"gene_symbol": "GYS1",
"hgnc_id": 4706,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1246A>G",
"hgvs_p": "p.Met416Val"
}
],
"clinvar_disease": "Glycogen storage disease due to muscle and heart glycogen synthase deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Glycogen storage disease due to muscle and heart glycogen synthase deficiency|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}