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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: 5-156647468-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=156647468&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 156647468,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000337851.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "NM_000337.6",
"protein_id": "NP_000328.2",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 619,
"cdna_end": null,
"cdna_length": 9383,
"mane_select": "ENST00000337851.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "ENST00000337851.9",
"protein_id": "ENSP00000338343.4",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 619,
"cdna_end": null,
"cdna_length": 9383,
"mane_select": "NM_000337.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Ala168Ala",
"transcript": "ENST00000435422.7",
"protein_id": "ENSP00000403003.2",
"transcript_support_level": 1,
"aa_start": 168,
"aa_end": null,
"aa_length": 289,
"cds_start": 504,
"cds_end": null,
"cds_length": 870,
"cdna_start": 991,
"cdna_end": null,
"cdna_length": 9755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Ala168Ala",
"transcript": "NM_001128209.2",
"protein_id": "NP_001121681.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 289,
"cds_start": 504,
"cds_end": null,
"cds_length": 870,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 9337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "NM_172244.3",
"protein_id": "NP_758447.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 256,
"cds_start": 507,
"cds_end": null,
"cds_length": 771,
"cdna_start": 619,
"cdna_end": null,
"cdna_length": 1166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "ENST00000517913.5",
"protein_id": "ENSP00000429378.1",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 256,
"cds_start": 507,
"cds_end": null,
"cds_length": 771,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 1412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "XM_005265966.6",
"protein_id": "XP_005266023.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 852,
"cdna_end": null,
"cdna_length": 9616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "XM_017009724.2",
"protein_id": "XP_016865213.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1464,
"cdna_end": null,
"cdna_length": 10228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "XM_047417518.1",
"protein_id": "XP_047273474.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1603,
"cdna_end": null,
"cdna_length": 10367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala",
"transcript": "XM_047417519.1",
"protein_id": "XP_047273475.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 290,
"cds_start": 507,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1954,
"cdna_end": null,
"cdna_length": 10718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Ala168Ala",
"transcript": "XM_047417520.1",
"protein_id": "XP_047273476.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 289,
"cds_start": 504,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1348,
"cdna_end": null,
"cdna_length": 10112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.502+52417G>A",
"hgvs_p": null,
"transcript": "XM_005265967.3",
"protein_id": "XP_005266024.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 175,
"cds_start": -4,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"dbsnp": "rs10071079",
"frequency_reference_population": 0.0012125309,
"hom_count_reference_population": 21,
"allele_count_reference_population": 1916,
"gnomad_exomes_af": 0.000672293,
"gnomad_genomes_af": 0.00628047,
"gnomad_exomes_ac": 960,
"gnomad_genomes_ac": 956,
"gnomad_exomes_homalt": 10,
"gnomad_genomes_homalt": 11,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.663,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000337851.9",
"gene_symbol": "SGCD",
"hgnc_id": 10807,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.507G>A",
"hgvs_p": "p.Ala169Ala"
}
],
"clinvar_disease": " recessive,Autosomal recessive limb-girdle muscular dystrophy type 2F,Cardiomyopathy,Dilated cardiomyopathy 1L,Inborn genetic diseases,Limb-girdle muscular dystrophy,Qualitative or quantitative defects of delta-sarcoglycan,SGCD-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:8",
"phenotype_combined": "not specified|Qualitative or quantitative defects of delta-sarcoglycan|not provided|Limb-girdle muscular dystrophy, recessive|Cardiomyopathy|Autosomal recessive limb-girdle muscular dystrophy type 2F|Inborn genetic diseases|Dilated cardiomyopathy 1L|Dilated cardiomyopathy 1L;Autosomal recessive limb-girdle muscular dystrophy type 2F|SGCD-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}