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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: 19-10835077-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=10835077&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 10835077,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006858.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.322G>C",
"hgvs_p": "p.Asp108His",
"transcript": "NM_006858.4",
"protein_id": "NP_006849.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 227,
"cds_start": 322,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000214869.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006858.4"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.322G>C",
"hgvs_p": "p.Asp108His",
"transcript": "ENST00000214869.7",
"protein_id": "ENSP00000214869.1",
"transcript_support_level": 1,
"aa_start": 108,
"aa_end": null,
"aa_length": 227,
"cds_start": 322,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006858.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000214869.7"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.208G>C",
"hgvs_p": "p.Asp70His",
"transcript": "XM_006722631.4",
"protein_id": "XP_006722694.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 189,
"cds_start": 208,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722631.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.-114G>C",
"hgvs_p": null,
"transcript": "ENST00000588289.1",
"protein_id": "ENSP00000464824.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 82,
"cds_start": null,
"cds_end": null,
"cds_length": 249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588289.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.282-14G>C",
"hgvs_p": null,
"transcript": "ENST00000589638.1",
"protein_id": "ENSP00000467690.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": null,
"cds_end": null,
"cds_length": 574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589638.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.281+179G>C",
"hgvs_p": null,
"transcript": "ENST00000591695.5",
"protein_id": "ENSP00000468294.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": null,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000591695.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.183+932G>C",
"hgvs_p": null,
"transcript": "ENST00000941053.1",
"protein_id": "ENSP00000611112.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": null,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941053.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "n.224G>C",
"hgvs_p": null,
"transcript": "ENST00000588259.5",
"protein_id": "ENSP00000468054.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000588259.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "n.287G>C",
"hgvs_p": null,
"transcript": "ENST00000591157.1",
"protein_id": "ENSP00000468492.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000591157.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "n.277G>C",
"hgvs_p": null,
"transcript": "NR_104015.2",
"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_104015.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"hgvs_c": "c.-75G>C",
"hgvs_p": null,
"transcript": "ENST00000586835.1",
"protein_id": "ENSP00000464856.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 64,
"cds_start": null,
"cds_end": null,
"cds_length": 195,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586835.1"
}
],
"gene_symbol": "TMED1",
"gene_hgnc_id": 17291,
"dbsnp": "rs762671844",
"frequency_reference_population": 6.8406e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8406e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9246876835823059,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.665,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9482,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.16,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006858.4",
"gene_symbol": "TMED1",
"hgnc_id": 17291,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.322G>C",
"hgvs_p": "p.Asp108His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}