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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: 12-116096697-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=116096697&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 116096697,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000281928.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Glu151Lys",
"transcript": "NM_015335.5",
"protein_id": "NP_056150.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 2210,
"cds_start": 451,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "ENST00000281928.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Glu151Lys",
"transcript": "ENST00000281928.9",
"protein_id": "ENSP00000281928.3",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 2210,
"cds_start": 451,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "NM_015335.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Glu151Lys",
"transcript": "ENST00000650226.1",
"protein_id": "ENSP00000496981.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 2222,
"cds_start": 451,
"cds_end": null,
"cds_length": 6669,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 8717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Glu141Lys",
"transcript": "ENST00000548743.2",
"protein_id": "ENSP00000448553.2",
"transcript_support_level": 3,
"aa_start": 141,
"aa_end": null,
"aa_length": 1080,
"cds_start": 421,
"cds_end": null,
"cds_length": 3244,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"transcript": "ENST00000647567.1",
"protein_id": "ENSP00000497136.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 436,
"cds_start": 361,
"cds_end": null,
"cds_length": 1312,
"cdna_start": 361,
"cdna_end": null,
"cdna_length": 1312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Glu151Lys",
"transcript": "XM_017019090.2",
"protein_id": "XP_016874579.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 2209,
"cds_start": 451,
"cds_end": null,
"cds_length": 6630,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 9882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Glu141Lys",
"transcript": "XM_047428605.1",
"protein_id": "XP_047284561.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 2200,
"cds_start": 421,
"cds_end": null,
"cds_length": 6603,
"cdna_start": 642,
"cdna_end": null,
"cdna_length": 9514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Glu141Lys",
"transcript": "XM_047428607.1",
"protein_id": "XP_047284563.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 2199,
"cds_start": 421,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 642,
"cdna_end": null,
"cdna_length": 9511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.49G>A",
"hgvs_p": "p.Glu17Lys",
"transcript": "XM_047428608.1",
"protein_id": "XP_047284564.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 2076,
"cds_start": 49,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 775,
"cdna_end": null,
"cdna_length": 9647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.49G>A",
"hgvs_p": "p.Glu17Lys",
"transcript": "XM_047428609.1",
"protein_id": "XP_047284565.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 2076,
"cds_start": 49,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 4145,
"cdna_end": null,
"cdna_length": 13017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.49G>A",
"hgvs_p": "p.Glu17Lys",
"transcript": "XM_047428610.1",
"protein_id": "XP_047284566.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 2076,
"cds_start": 49,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 1942,
"cdna_end": null,
"cdna_length": 10814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.49G>A",
"hgvs_p": "p.Glu17Lys",
"transcript": "XM_047428611.1",
"protein_id": "XP_047284567.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 2076,
"cds_start": 49,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 2038,
"cdna_end": null,
"cdna_length": 10910,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.215G>A",
"hgvs_p": null,
"transcript": "ENST00000648737.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"dbsnp": "rs773315749",
"frequency_reference_population": 0.000019208892,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000205231,
"gnomad_genomes_af": 0.00000657592,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.21594086289405823,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.284,
"revel_prediction": "Benign",
"alphamissense_score": 0.0991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.643,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000281928.9",
"gene_symbol": "MED13L",
"hgnc_id": 22962,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.451G>A",
"hgvs_p": "p.Glu151Lys"
}
],
"clinvar_disease": " dextro-looped,Transposition of the great arteries",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Transposition of the great arteries, dextro-looped",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}